diff --git a/.gitmodules b/.gitmodules index 751b25affdf22d62f3c53ae674df67c07e042063..ed58816a5f19be8e9028c6d91d163321dce1c3fd 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,7 +1,3 @@ -[submodule "github-crawler"] - path = github-crawler - url = https://gitlab.liris.cnrs.fr/sharefair/github-crawler.git - branch = BioFlow-Insight-corpus [submodule "bioflow-insight"] path = bioflow-insight url = https://gitlab.liris.cnrs.fr/sharefair/bioflow-insight.git diff --git a/README.md b/README.md index 4b59e19727da8410b0672eb5180050ad2bd52535..d97317b007ac1a3a8567df74fe41242c8ee93319 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,9 @@ To run the analysis simply, clone the repository by running this command : Then simply execute the Python notebook. -> Important: Even though the code presented here allows for obtaining the results of the analysis of the large dataset of workflows, including downloading and analyzing the workflows, it does not necessarily guarantee full reproducibility. Since the workflows are downloaded from GitHub, they can continue to evolve (e.g., updates or modifications, or even deletion). In such cases, the results may vary. For the results presented in the paper, the workflows were downloaded on the 16th of February 2024. +> `unzip` might have to be installed. But it can be replaced by an equivalent tool. + +> Note : To install graphviz, in linux you might need to execute this command `sudo apt install graphviz` <!--`git submodule update --recursive --remote`--> diff --git a/bioflow-insight b/bioflow-insight index 7b53b437a663d9ec4e70dc9e259b1731b5627639..2a05d2056ad2e1fcff4892563d3c0bba51dcef2c 160000 --- a/bioflow-insight +++ b/bioflow-insight @@ -1 +1 @@ -Subproject commit 7b53b437a663d9ec4e70dc9e259b1731b5627639 +Subproject commit 2a05d2056ad2e1fcff4892563d3c0bba51dcef2c diff --git a/different_errors_detected.csv b/different_errors_detected.csv index 9eb6d79c6862a5f6a5cfe26b5ccd4297c5d7f302..b00ffdcdc71c8a5d270c4e197115ae103fb13ba9 100644 --- a/different_errors_detected.csv +++ b/different_errors_detected.csv @@ -6,7 +6,7 @@ Tried to access an emit even though the element its emitting has not been called Tried to include a file which doesn't exist 14 An include was present in a main or subworkflow 1 In a pipe operator, the first thing called does not exist 11 -Syntax error in the code (e.g. not the same of parentheses) 35 +Syntax error in the code (e.g. not the same of parentheses) 34 Element (process or subworkflow) is expected to be defined in a file but is not 8 A subworkflow either emits nothing or too many values for use in an operation 20 A subworkflow or process was defined badly (e.g. multiple input sections, multiple main sections...) 10 diff --git a/failed_2_analyse.txt b/failed_2_analyse.txt index f5e9fea70a9424d1c6d1ff4cf322276e2a63281a..39c26f5b360141b00492e1b4d9337b47f6aba5a0 100644 --- a/failed_2_analyse.txt +++ b/failed_2_analyse.txt @@ -1,78 +1,78 @@ -- 9 ../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP - [10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/nf-iap.nf': Something went wrong in an include, possibly at line 88. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/NextflowModules/Utils/fastq.nf'. +- 9 Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP + [10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/nf-iap.nf': Something went wrong in an include, possibly at line 88. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/NextflowModules/Utils/fastq.nf'. -- 10 ../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS - [10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/WGS.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/NextflowModules/Utils/fastq.nf'. +- 10 Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS + [10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/WGS.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/NextflowModules/Utils/fastq.nf'. -- 11 ../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES - [10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/WES_Fingerprint.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/NextflowModules/Utils/bam.nf'. +- 11 Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES + [10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/WES_Fingerprint.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/NextflowModules/Utils/bam.nf'. -- 16 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis - [3] Error in the file '../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis/workflows/aradeepopsis.nf': Don't know how to handle '( params.masks ? MASKS : SEGMENT )' in a pipe operator, possibly at line 56. Try using the recommended operator composition. +- 16 Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis + [3] Error in the file 'Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis/workflows/aradeepopsis.nf': Don't know how to handle '( params.masks ? MASKS : SEGMENT )' in a pipe operator, possibly at line 56. Try using the recommended operator composition. -- 24 ../../../Workflow-Corpus-Open-License/brwnj/smoove-nf - [5] Error in the file '../../../Workflow-Corpus-Open-License/brwnj/smoove-nf/main.nf': A ternary conditional operator was used with an tuple, possibly at line 297. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way. +- 24 Workflow-Corpus-Open-License/brwnj/smoove-nf + [5] Error in the file 'Workflow-Corpus-Open-License/brwnj/smoove-nf/main.nf': A ternary conditional operator was used with an tuple, possibly at line 297. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way. -- 26 ../../../Workflow-Corpus-Open-License/brwnj/covviz - [5] Error in the file '../../../Workflow-Corpus-Open-License/brwnj/covviz/main.nf': A ternary conditional operator was used with an tuple, possibly at line 125. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way. +- 26 Workflow-Corpus-Open-License/brwnj/covviz + [5] Error in the file 'Workflow-Corpus-Open-License/brwnj/covviz/main.nf': A ternary conditional operator was used with an tuple, possibly at line 125. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way. -- 34 ../../../Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen - [4] Error in the file '../../../Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen/workflows/bacterial_base.nf': 'quast' is trying to be created as a channel, possibly at line 16. It already exists as a process or a subworkflow in the nextflow file. +- 34 Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen + [4] Error in the file 'Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen/workflows/bacterial_base.nf': 'quast' is trying to be created as a channel, possibly at line 16. It already exists as a process or a subworkflow in the nextflow file. -- 41 ../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline - [2] Error in the file '../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline/workflows/cmgg-germline.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 250. +- 41 Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline + [2] Error in the file 'Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline/workflows/cmgg-germline.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 250. -- 42 ../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural - [2] Error in the file '../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural/workflows/cmgg-structural.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 135. +- 42 Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural + [2] Error in the file 'Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural/workflows/cmgg-structural.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 135. -- 47 ../../../Workflow-Corpus-Open-License/jnoms/virID - [14] Error in the file '../../../Workflow-Corpus-Open-License/jnoms/virID/virID.nf': 'bwa_mem_contigs' is neither a process, subworkflow or an operator. In the executor 'contigs +- 47 Workflow-Corpus-Open-License/jnoms/virID + [14] Error in the file 'Workflow-Corpus-Open-License/jnoms/virID/virID.nf': 'bwa_mem_contigs' is neither a process, subworkflow or an operator. In the executor 'contigs .join(process_read_pairs.out) | bwa_mem_contigs'. -- 54 ../../../Workflow-Corpus-Open-License/replikation/What_the_Phage - [10] Error in the file '../../../Workflow-Corpus-Open-License/replikation/What_the_Phage/phage_deprecated.nf': Something went wrong in an include, possibly at line 135. No such file: '../../../Workflow-Corpus-Open-License/replikation/What_the_Phage/modules/checkV.nf'. +- 54 Workflow-Corpus-Open-License/replikation/What_the_Phage + [10] Error in the file 'Workflow-Corpus-Open-License/replikation/What_the_Phage/phage_deprecated.nf': Something went wrong in an include, possibly at line 135. No such file: 'Workflow-Corpus-Open-License/replikation/What_the_Phage/modules/checkV.nf'. -- 55 ../../../Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA - [20] Error in the file '../../../Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA/main.nf': To much to unpack : The subworkflow 'VALIDATE_FASTQS_WF' emits over one channel in a operation, possibly at line 31. +- 55 Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA + [20] Error in the file 'Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA/main.nf': To much to unpack : The subworkflow 'VALIDATE_FASTQS_WF' emits over one channel in a operation, possibly at line 31. -- 59 ../../../Workflow-Corpus-Open-License/Hammarn/Nextflow_test - [16] Error in the file '../../../Workflow-Corpus-Open-License/Hammarn/Nextflow_test/main.nf': No 'main' workflow was found. +- 59 Workflow-Corpus-Open-License/Hammarn/Nextflow_test + [16] Error in the file 'Workflow-Corpus-Open-License/Hammarn/Nextflow_test/main.nf': No 'main' workflow was found. -- 61 ../../../Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt - [16] Error in the file '../../../Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt/main.nf': No 'main' workflow was found. +- 61 Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt + [16] Error in the file 'Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt/main.nf': No 'main' workflow was found. -- 64 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis - [10] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/main.nf': Something went wrong in an include, possibly at line 17. No such file: '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/modules/data/test_train_split/test_train_split.nf'. +- 64 Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis + [10] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/main.nf': Something went wrong in an include, possibly at line 17. No such file: 'Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/modules/data/test_train_split/test_train_split.nf'. -- 65 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern - [16] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern/workflow.nf': No 'main' workflow was found. +- 65 Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern + [16] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern/workflow.nf': No 'main' workflow was found. -- 66 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search - [16] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search/stacked_ensemble_grid_search.nf': No 'main' workflow was found. +- 66 Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search + [16] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search/stacked_ensemble_grid_search.nf': No 'main' workflow was found. -- 67 ../../../Workflow-Corpus-Open-License/mgimenez720/plaSquid - [2] Error in the file '../../../Workflow-Corpus-Open-License/mgimenez720/plaSquid/workflows/RIPsearch.nf': Not the same number of parameters given as input for the process 'FilterDom', possibly at line 49. +- 67 Workflow-Corpus-Open-License/mgimenez720/plaSquid + [2] Error in the file 'Workflow-Corpus-Open-License/mgimenez720/plaSquid/workflows/RIPsearch.nf': Not the same number of parameters given as input for the process 'FilterDom', possibly at line 49. -- 68 ../../../Workflow-Corpus-Open-License/bahlolab/PLASTER - [18] Error in the file '../../../Workflow-Corpus-Open-License/bahlolab/PLASTER/nf/functions.nf': 'path' is expected to be defined in the file, but it could not be found. +- 68 Workflow-Corpus-Open-License/bahlolab/PLASTER + [18] Error in the file 'Workflow-Corpus-Open-License/bahlolab/PLASTER/nf/functions.nf': 'path' is expected to be defined in the file, but it could not be found. -- 70 ../../../Workflow-Corpus-Open-License/EpiDiverse/ewas - [9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/ewas/main.nf': A tuple is associated with an call, possibly at line 283. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. +- 70 Workflow-Corpus-Open-License/EpiDiverse/ewas + [9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/ewas/main.nf': A tuple is associated with an call, possibly at line 283. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. -- 71 ../../../Workflow-Corpus-Open-License/EpiDiverse/wgbs - [9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/wgbs/main.nf': A tuple is associated with an call, possibly at line 166. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. +- 71 Workflow-Corpus-Open-License/EpiDiverse/wgbs + [9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/wgbs/main.nf': A tuple is associated with an call, possibly at line 166. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. -- 72 ../../../Workflow-Corpus-Open-License/EpiDiverse/dmr - [9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/dmr/main.nf': A tuple is associated with an call, possibly at line 210. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. +- 72 Workflow-Corpus-Open-License/EpiDiverse/dmr + [9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/dmr/main.nf': A tuple is associated with an call, possibly at line 210. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. -- 80 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling - [10] Error in the file '../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/main.nf': Something went wrong in an include, possibly at line 7. No such file: '../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/nf-core-modules/modules/nf-core/samtools/merge/main.nf'. +- 80 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling + [10] Error in the file 'Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/main.nf': Something went wrong in an include, possibly at line 7. No such file: 'Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/nf-core-modules/modules/nf-core/samtools/merge/main.nf'. -- 86 ../../../Workflow-Corpus-Open-License/data-intuitive/diflow - [16] Error in the file '../../../Workflow-Corpus-Open-License/data-intuitive/diflow/main.nf': No 'main' workflow was found. +- 86 Workflow-Corpus-Open-License/data-intuitive/diflow + [16] Error in the file 'Workflow-Corpus-Open-License/data-intuitive/diflow/main.nf': No 'main' workflow was found. -- 92 ../../../Workflow-Corpus-Open-License/sanger-tol/blobtoolkit - [14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/blobtoolkit/subworkflows/local/minimap_alignment.nf': 'set { ch_aligned }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() +- 92 Workflow-Corpus-Open-License/sanger-tol/blobtoolkit + [14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/blobtoolkit/subworkflows/local/minimap_alignment.nf': 'set { ch_aligned }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() | mix ( MINIMAP2_HIC.out.bam ) | mix ( MINIMAP2_ILMN.out.bam ) | mix ( MINIMAP2_CCS.out.bam ) @@ -80,287 +80,284 @@ | mix ( MINIMAP2_ONT.out.bam ) | set { ch_aligned }', possibly at line 68. -- 93 ../../../Workflow-Corpus-Open-License/sanger-tol/sequencecomposition - [8] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/sequencecomposition/subworkflows/local/fasta_windows.nf': The call for 'TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) )' coudn't be found, before its use in the operation 'ch_compressed_bed = TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) ).output', possibly at line 67. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 93 Workflow-Corpus-Open-License/sanger-tol/sequencecomposition + [8] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/sequencecomposition/subworkflows/local/fasta_windows.nf': The call for 'TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) )' coudn't be found, before its use in the operation 'ch_compressed_bed = TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) ).output', possibly at line 67. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 98 ../../../Workflow-Corpus-Open-License/sanger-tol/readmapping - [14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/readmapping/subworkflows/local/prepare_genome.nf': 'set { ch_bwamem }' is neither a process, subworkflow or an operator. In the executor 'Channel.fromPath ( params.bwamem2_index ) +- 98 Workflow-Corpus-Open-License/sanger-tol/readmapping + [14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/readmapping/subworkflows/local/prepare_genome.nf': 'set { ch_bwamem }' is neither a process, subworkflow or an operator. In the executor 'Channel.fromPath ( params.bwamem2_index ) | combine ( ch_fasta ) | map { bwa, meta, fa -> [ meta, bwa ] } | set { ch_bwamem }', possibly at line 39. -- 99 ../../../Workflow-Corpus-Open-License/sanger-tol/genomenote - [14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/genomenote/subworkflows/local/genome_statistics.nf': 'set { ch_fastk }' is neither a process, subworkflow or an operator. In the executor 'ch_pacbio.file +- 99 Workflow-Corpus-Open-License/sanger-tol/genomenote + [14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/genomenote/subworkflows/local/genome_statistics.nf': 'set { ch_fastk }' is neither a process, subworkflow or an operator. In the executor 'ch_pacbio.file | map { meta, bam -> [ meta + [ id: meta.id.split('_')[0..-2].join('_') ], bam ] } | groupTuple ( by: [0] ) | set { ch_fastk }', possibly at line 62. -- 101 ../../../Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline - [4] Error in the file '../../../Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline/gwas.nf': 'pcrelate' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 101 Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline + [4] Error in the file 'Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline/gwas.nf': 'pcrelate' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 110 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 110 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf + [4] Error in the file 'Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 111 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT - [4] Error in the file '../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 111 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT + [4] Error in the file 'Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 118 ../../../Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow - [16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. +- 118 Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow + [16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. -- 119 ../../../Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow - [16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. +- 119 Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow + [16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. -- 120 ../../../Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow - [16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. +- 120 Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow + [16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file. -- 121 ../../../Workflow-Corpus-Open-License/SamStudio8/elan-nextflow - [2] Error in the file '../../../Workflow-Corpus-Open-License/SamStudio8/elan-nextflow/workflows/elan.nf': Not the same number of parameters given as input for the process 'announce_uploads', possibly at line 14. +- 121 Workflow-Corpus-Open-License/SamStudio8/elan-nextflow + [2] Error in the file 'Workflow-Corpus-Open-License/SamStudio8/elan-nextflow/workflows/elan.nf': Not the same number of parameters given as input for the process 'announce_uploads', possibly at line 14. -- 123 ../../../Workflow-Corpus-Open-License/robsyme/nf-repeatmasking - [4] Error in the file '../../../Workflow-Corpus-Open-License/robsyme/nf-repeatmasking/main.nf': 'recentLTRs' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 123 Workflow-Corpus-Open-License/robsyme/nf-repeatmasking + [4] Error in the file 'Workflow-Corpus-Open-License/robsyme/nf-repeatmasking/main.nf': 'recentLTRs' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 125 ../../../Workflow-Corpus-Open-License/TARGENE/targene-pipeline - [20] Error in the file '../../../Workflow-Corpus-Open-License/TARGENE/targene-pipeline/workflows/targene.nf': The subworkflow 'SVPWorkflow' doesn't emit anything. It is given to an operation, possibly at line 71. +- 125 Workflow-Corpus-Open-License/TARGENE/targene-pipeline + [20] Error in the file 'Workflow-Corpus-Open-License/TARGENE/targene-pipeline/workflows/targene.nf': The subworkflow 'SVPWorkflow' doesn't emit anything. It is given to an operation, possibly at line 71. -- 130 ../../../Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline - [9] Error in the file '../../../Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline/pipeline.nf': A tuple is associated with an call, possibly at line 288. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. +- 130 Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline + [9] Error in the file 'Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline/pipeline.nf': A tuple is associated with an call, possibly at line 288. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. -- 133 ../../../Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning - [9] Error in the file '../../../Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning/gnn_pipeline.nf': A tuple is associated with an call, possibly at line 34. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. +- 133 Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning + [9] Error in the file 'Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning/gnn_pipeline.nf': A tuple is associated with an call, possibly at line 34. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way. -- 134 ../../../Workflow-Corpus-Open-License/AndersenLab/ril-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/AndersenLab/ril-nf/main.nf': 'fq_coverage' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 134 Workflow-Corpus-Open-License/AndersenLab/ril-nf + [4] Error in the file 'Workflow-Corpus-Open-License/AndersenLab/ril-nf/main.nf': 'fq_coverage' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 135 ../../../Workflow-Corpus-Open-License/AndersenLab/alignment-nf - [14] Error in the file '../../../Workflow-Corpus-Open-License/AndersenLab/alignment-nf/main.nf': '(coverage_id & idxstats_id & flagstat_id & stats_id)' is neither a process, subworkflow or an operator. In the executor 'alignment.out.map { row, bam, bai -> ["id", row.id, bam, bai ]} | (coverage_id & idxstats_id & flagstat_id & stats_id)'. +- 135 Workflow-Corpus-Open-License/AndersenLab/alignment-nf + [14] Error in the file 'Workflow-Corpus-Open-License/AndersenLab/alignment-nf/main.nf': '(coverage_id & idxstats_id & flagstat_id & stats_id)' is neither a process, subworkflow or an operator. In the executor 'alignment.out.map { row, bam, bai -> ["id", row.id, bam, bai ]} | (coverage_id & idxstats_id & flagstat_id & stats_id)'. -- 144 ../../../Workflow-Corpus-Open-License/phac-nml/mikrokondo - [20] Error in the file '../../../Workflow-Corpus-Open-License/phac-nml/mikrokondo/main.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 87. +- 144 Workflow-Corpus-Open-License/phac-nml/mikrokondo + [20] Error in the file 'Workflow-Corpus-Open-License/phac-nml/mikrokondo/main.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 87. -- 161 ../../../Workflow-Corpus-Open-License/CDCgov/mycosnp-nf - [18] Error in the file '../../../Workflow-Corpus-Open-License/CDCgov/mycosnp-nf/subworkflows/local/snpeff_build.nf': 'SNPEFF_BUILD' is expected to be defined in the file, but it could not be found. +- 161 Workflow-Corpus-Open-License/CDCgov/mycosnp-nf + [18] Error in the file 'Workflow-Corpus-Open-License/CDCgov/mycosnp-nf/subworkflows/local/snpeff_build.nf': 'SNPEFF_BUILD' is expected to be defined in the file, but it could not be found. -- 162 ../../../Workflow-Corpus-Open-License/CDCgov/tostadas - [2] Error in the file '../../../Workflow-Corpus-Open-License/CDCgov/tostadas/workflows/tostadas.nf': Not the same number of parameters given as input for the process 'UPDATE_SUBMISSION', possibly at line 203. +- 162 Workflow-Corpus-Open-License/CDCgov/tostadas + [2] Error in the file 'Workflow-Corpus-Open-License/CDCgov/tostadas/workflows/tostadas.nf': Not the same number of parameters given as input for the process 'UPDATE_SUBMISSION', possibly at line 203. -- 164 ../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines - [10] Error in the file '../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/workflows/spatial.nf': Something went wrong in an include, possibly at line 46. No such file: '../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/modules/bayestme/nextflow/subworkflows/bayestme/bayestme_basic_visium_analysis/main.nf'. +- 164 Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines + [10] Error in the file 'Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/workflows/spatial.nf': Something went wrong in an include, possibly at line 46. No such file: 'Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/modules/bayestme/nextflow/subworkflows/bayestme/bayestme_basic_visium_analysis/main.nf'. -- 167 ../../../Workflow-Corpus-Open-License/cbcrg/msa-af2-nf - [8] Error in the file '../../../Workflow-Corpus-Open-License/cbcrg/msa-af2-nf/main.nf': The call for 'run_seq_aln' coudn't be found, before its use in the operation 'run_seq_aln.out.seq_aln_output.combine(run_psicoffee.out.psicoffee_output, by: 0).combine(dssp_to_fasta.out.dssp_output, by: 0).combine(run_struct_aln.out.struct_output, by: 0).combine(templates, by: 0).combine(structures, by: 0).combine(run_alphafold2.out.af2_models.groupTuple(), by: 0).set{comp_and_eval_input}', possibly at line 73. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 167 Workflow-Corpus-Open-License/cbcrg/msa-af2-nf + [8] Error in the file 'Workflow-Corpus-Open-License/cbcrg/msa-af2-nf/main.nf': The call for 'run_seq_aln' coudn't be found, before its use in the operation 'run_seq_aln.out.seq_aln_output.combine(run_psicoffee.out.psicoffee_output, by: 0).combine(dssp_to_fasta.out.dssp_output, by: 0).combine(run_struct_aln.out.struct_output, by: 0).combine(templates, by: 0).combine(structures, by: 0).combine(run_alphafold2.out.af2_models.groupTuple(), by: 0).set{comp_and_eval_input}', possibly at line 73. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 168 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20 - [16] Error in the file '../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20/rnaseq-flow.nf': No 'main' workflow was found. +- 168 Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20 + [16] Error in the file 'Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20/rnaseq-flow.nf': No 'main' workflow was found. -- 179 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines - [8] Error in the file '../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines/subworkflows/hs_pta.nf': The call for 'PICARD_MARKDUPLICATES' coudn't be found, before its use in the operation 'apply_bqsr = PICARD_MARKDUPLICATES.out.dedup_bam.join(GATK_BASERECALIBRATOR.out.table)', possibly at line 175. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 179 Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines + [8] Error in the file 'Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines/subworkflows/hs_pta.nf': The call for 'PICARD_MARKDUPLICATES' coudn't be found, before its use in the operation 'apply_bqsr = PICARD_MARKDUPLICATES.out.dedup_bam.join(GATK_BASERECALIBRATOR.out.table)', possibly at line 175. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 187 ../../../Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing - [16] Error in the file '../../../Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing/main.nf': No 'main' workflow was found. +- 187 Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing + [16] Error in the file 'Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing/main.nf': No 'main' workflow was found. -- 192 ../../../Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules - [16] Error in the file '../../../Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules/bacteria-example.nf': No 'main' workflow was found. +- 192 Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules + [16] Error in the file 'Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules/bacteria-example.nf': No 'main' workflow was found. -- 213 ../../../Workflow-Corpus-Open-License/aertslab/SpatialNF - [16] Error in the file '../../../Workflow-Corpus-Open-License/aertslab/SpatialNF/main.nf': No 'main' workflow was found. +- 213 Workflow-Corpus-Open-License/aertslab/SpatialNF + [16] Error in the file 'Workflow-Corpus-Open-License/aertslab/SpatialNF/main.nf': No 'main' workflow was found. -- 216 ../../../Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert - [22] Error in the file '../../../Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert/modules/processes.nf': Multiple 'input:' were found in the process 'Convert_EachFileFromRoot2SeparateOMETIFF'. +- 216 Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert + [22] Error in the file 'Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert/modules/processes.nf': Multiple 'input:' were found in the process 'Convert_EachFileFromRoot2SeparateOMETIFF'. -- 219 ../../../Workflow-Corpus-Open-License/lepsalex/results - [16] Error in the file '../../../Workflow-Corpus-Open-License/lepsalex/results/debug/calls.nf': No 'main' workflow was found. +- 220 Workflow-Corpus-Open-License/HadrienG/nanoflow + [4] Error in the file 'Workflow-Corpus-Open-License/HadrienG/nanoflow/main.nf': 'assembly' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 221 ../../../Workflow-Corpus-Open-License/HadrienG/nanoflow - [4] Error in the file '../../../Workflow-Corpus-Open-License/HadrienG/nanoflow/main.nf': 'assembly' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 221 Workflow-Corpus-Open-License/HadrienG/nextflow_rna + [16] Error in the file 'Workflow-Corpus-Open-License/HadrienG/nextflow_rna/rna.nf': No 'main' workflow was found. -- 222 ../../../Workflow-Corpus-Open-License/HadrienG/nextflow_rna - [16] Error in the file '../../../Workflow-Corpus-Open-License/HadrienG/nextflow_rna/rna.nf': No 'main' workflow was found. +- 222 Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support + [16] Error in the file 'Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support/functions.nf': No 'main' workflow was found. -- 223 ../../../Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support - [16] Error in the file '../../../Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support/functions.nf': No 'main' workflow was found. +- 227 Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline + [2] Error in the file 'Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline/virify.nf': Not the same number of parameters given as input for the subworklfow 'annotate' in the call, possibly at line 649. -- 228 ../../../Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline - [2] Error in the file '../../../Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline/virify.nf': Not the same number of parameters given as input for the subworklfow 'annotate' in the call, possibly at line 649. +- 228 Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc + [22] Error in the file 'Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc/modules/local/custom.nf': Multiple 'output:' were found in the process 'processGVCF'? -- 229 ../../../Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc - [22] Error in the file '../../../Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc/modules/local/custom.nf': Multiple 'output:' were found in the process 'processGVCF'? +- 230 Workflow-Corpus-Open-License/B-UMMI/DEN-IM + [4] Error in the file 'Workflow-Corpus-Open-License/B-UMMI/DEN-IM/DEN-IM.nf': 'compile_status_buffer' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 231 ../../../Workflow-Corpus-Open-License/B-UMMI/DEN-IM - [4] Error in the file '../../../Workflow-Corpus-Open-License/B-UMMI/DEN-IM/DEN-IM.nf': 'compile_status_buffer' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 236 Workflow-Corpus-Open-License/jemunro/Tidy-nf + [16] Error in the file 'Workflow-Corpus-Open-License/jemunro/Tidy-nf/example.nf': No 'main' workflow was found. -- 237 ../../../Workflow-Corpus-Open-License/jemunro/Tidy-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/jemunro/Tidy-nf/example.nf': No 'main' workflow was found. +- 240 Workflow-Corpus-Open-License/fmalmeida/MpGAP + [22] Error in the file 'Workflow-Corpus-Open-License/fmalmeida/MpGAP/workflows/hybrid.nf': Multiple 'main:' were found in the subworkflow 'HYBRID'. -- 241 ../../../Workflow-Corpus-Open-License/fmalmeida/MpGAP - [22] Error in the file '../../../Workflow-Corpus-Open-License/fmalmeida/MpGAP/workflows/hybrid.nf': Multiple 'main:' were found in the subworkflow 'HYBRID'. +- 248 Workflow-Corpus-Open-License/biocorecrg/contamination-nf + [16] Error in the file 'Workflow-Corpus-Open-License/biocorecrg/contamination-nf/main.nf': Not the same number of opening and closing curlies '{}' in the file. -- 249 ../../../Workflow-Corpus-Open-License/biocorecrg/contamination-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/biocorecrg/contamination-nf/main.nf': Not the same number of opening and closing curlies '{}' in the file. +- 253 Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW + [16] Error in the file 'Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW/align.nf': Not the same number of opening and closing curlies '{}' in the file. -- 254 ../../../Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW - [16] Error in the file '../../../Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW/align.nf': Not the same number of opening and closing curlies '{}' in the file. +- 256 Workflow-Corpus-Open-License/nextflow-io/nf-ffq + [16] Error in the file 'Workflow-Corpus-Open-License/nextflow-io/nf-ffq/ffq.nf': No 'main' workflow was found. -- 257 ../../../Workflow-Corpus-Open-License/nextflow-io/nf-ffq - [16] Error in the file '../../../Workflow-Corpus-Open-License/nextflow-io/nf-ffq/ffq.nf': No 'main' workflow was found. +- 257 Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21 + [10] Error in the file 'Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/main.nf': Something went wrong in an include, possibly at line 76. No such file: 'Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/${subwork_folder}/fastqc.nf'. -- 258 ../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21 - [10] Error in the file '../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/main.nf': Something went wrong in an include, possibly at line 76. No such file: '../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/${subwork_folder}/fastqc.nf'. +- 272 Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy + [10] Error in the file 'Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: 'Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'. -- 273 ../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy - [10] Error in the file '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'. +- 273 Workflow-Corpus-Open-License/hoelzer-lab/rnaflow + [4] Error in the file 'Workflow-Corpus-Open-License/hoelzer-lab/rnaflow/main.nf': 'sortmerna' is trying to be created as a channel, possibly at line 475. It already exists as a process or a subworkflow in the nextflow file. -- 274 ../../../Workflow-Corpus-Open-License/hoelzer-lab/rnaflow - [4] Error in the file '../../../Workflow-Corpus-Open-License/hoelzer-lab/rnaflow/main.nf': 'sortmerna' is trying to be created as a channel, possibly at line 475. It already exists as a process or a subworkflow in the nextflow file. +- 277 Workflow-Corpus-Open-License/bschiffthaler/nf-modules + [16] Error in the file 'Workflow-Corpus-Open-License/bschiffthaler/nf-modules/multiqc.nf': No 'main' workflow was found. -- 278 ../../../Workflow-Corpus-Open-License/bschiffthaler/nf-modules - [16] Error in the file '../../../Workflow-Corpus-Open-License/bschiffthaler/nf-modules/multiqc.nf': No 'main' workflow was found. +- 294 Workflow-Corpus-Open-License/bactopia/bactopia + [10] Error in the file 'Workflow-Corpus-Open-License/bactopia/bactopia/workflows/teton.nf': Something went wrong in an include, possibly at line 33. No such file: 'Workflow-Corpus-Open-License/bactopia/bactopia/modules/local/bactopia/gather_samples/main.nf'. -- 295 ../../../Workflow-Corpus-Open-License/bactopia/bactopia - [10] Error in the file '../../../Workflow-Corpus-Open-License/bactopia/bactopia/workflows/teton.nf': Something went wrong in an include, possibly at line 33. No such file: '../../../Workflow-Corpus-Open-License/bactopia/bactopia/modules/local/bactopia/gather_samples/main.nf'. +- 295 Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis + [18] Error in the file 'Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis/modules/nf-core/modules/blast/makeblastdb/main.nf': 'SIGS_BLAST_MAKEBLASTDB' is expected to be defined in the file, but it could not be found. -- 296 ../../../Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis - [18] Error in the file '../../../Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis/modules/nf-core/modules/blast/makeblastdb/main.nf': 'SIGS_BLAST_MAKEBLASTDB' is expected to be defined in the file, but it could not be found. +- 299 Workflow-Corpus-Open-License/esteinig/nf-mvp + [18] Error in the file 'Workflow-Corpus-Open-License/esteinig/nf-mvp/lib/utils.nf': 'getSubsampleReads' is expected to be defined in the file, but it could not be found. -- 300 ../../../Workflow-Corpus-Open-License/esteinig/nf-mvp - [18] Error in the file '../../../Workflow-Corpus-Open-License/esteinig/nf-mvp/lib/utils.nf': 'getSubsampleReads' is expected to be defined in the file, but it could not be found. +- 304 Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines + [16] Error in the file 'Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines/main.nf': No 'main' workflow was found. -- 305 ../../../Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines - [16] Error in the file '../../../Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines/main.nf': No 'main' workflow was found. +- 306 Workflow-Corpus-Open-License/dmalzl/howto-nf + [18] Error in the file 'Workflow-Corpus-Open-License/dmalzl/howto-nf/workflows/chipseq.nf': 'CHIPSEQ' is expected to be defined in the file, but it could not be found. -- 307 ../../../Workflow-Corpus-Open-License/dmalzl/howto-nf - [18] Error in the file '../../../Workflow-Corpus-Open-License/dmalzl/howto-nf/workflows/chipseq.nf': 'CHIPSEQ' is expected to be defined in the file, but it could not be found. +- 311 Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training + [4] Error in the file 'Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training/main.nf': 'srst2_resistance' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 312 ../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training - [4] Error in the file '../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training/main.nf': 'srst2_resistance' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 325 Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice + [22] Error in the file 'Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice/somatic_vardict_pindel.nf': Multiple 'when:' were found in the process 'cnv_oncocnv_tumor_controls'. -- 326 ../../../Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice - [22] Error in the file '../../../Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice/somatic_vardict_pindel.nf': Multiple 'when:' were found in the process 'cnv_oncocnv_tumor_controls'. +- 337 Workflow-Corpus-Open-License/jtmccr1/beast_analysis + [22] Error in the file 'Workflow-Corpus-Open-License/jtmccr1/beast_analysis/beast_analysis.nf': Multiple 'input:' were found in the process 'mcc'. -- 338 ../../../Workflow-Corpus-Open-License/jtmccr1/beast_analysis - [22] Error in the file '../../../Workflow-Corpus-Open-License/jtmccr1/beast_analysis/beast_analysis.nf': Multiple 'input:' were found in the process 'mcc'. +- 344 Workflow-Corpus-Open-License/bguo068/posseleff_empirical + [2] Error in the file 'Workflow-Corpus-Open-License/bguo068/posseleff_empirical/01_filter_vcf.nf': Not the same number of parameters given as input for the process 'BCFTOOLS_VIEW_FILTER_SAMPLE_BY_IMISS1', possibly at line 165. -- 345 ../../../Workflow-Corpus-Open-License/bguo068/posseleff_empirical - [2] Error in the file '../../../Workflow-Corpus-Open-License/bguo068/posseleff_empirical/01_filter_vcf.nf': Not the same number of parameters given as input for the process 'BCFTOOLS_VIEW_FILTER_SAMPLE_BY_IMISS1', possibly at line 165. +- 349 Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia + [14] Error in the file 'Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia/subworkflows/encyclopedia.nf': 'set { global_files }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() | set { global_files }', possibly at line 89. -- 350 ../../../Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia - [14] Error in the file '../../../Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia/subworkflows/encyclopedia.nf': 'set { global_files }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() | set { global_files }', possibly at line 89. +- 353 Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines + [16] Error in the file 'Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines/main.nf': Not the same number of opening and closing parentheses '()' in the file. -- 354 ../../../Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines - [16] Error in the file '../../../Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines/main.nf': Not the same number of opening and closing parentheses '()' in the file. +- 355 Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline + [4] Error in the file 'Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline/main.nf': 'hardfilters_snp' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 356 ../../../Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline - [4] Error in the file '../../../Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline/main.nf': 'hardfilters_snp' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 356 Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow + [2] Error in the file 'Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow/subworkflows/abinitio_training/main.nf': Not the same number of parameters given as input for the process 'BLAST_BLASTP', possibly at line 54. -- 357 ../../../Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow - [2] Error in the file '../../../Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow/subworkflows/abinitio_training/main.nf': Not the same number of parameters given as input for the process 'BLAST_BLASTP', possibly at line 54. +- 368 Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline + [16] Error in the file 'Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline/rnaseq_script.nf': No 'main' workflow was found. -- 369 ../../../Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline - [16] Error in the file '../../../Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline/rnaseq_script.nf': No 'main' workflow was found. +- 382 Workflow-Corpus-Open-License/PavriLab/hicer-nf + [20] Error in the file 'Workflow-Corpus-Open-License/PavriLab/hicer-nf/workflows/hicer.nf': To much to unpack : The subworkflow 'PREPARE_GENOME' emits over one channel in a operation, possibly at line 146. -- 383 ../../../Workflow-Corpus-Open-License/PavriLab/hicer-nf - [20] Error in the file '../../../Workflow-Corpus-Open-License/PavriLab/hicer-nf/workflows/hicer.nf': To much to unpack : The subworkflow 'PREPARE_GENOME' emits over one channel in a operation, possibly at line 146. +- 385 Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo + [4] Error in the file 'Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file. -- 386 ../../../Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo - [4] Error in the file '../../../Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file. +- 393 Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf + [4] Error in the file 'Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf/main.nf': 'arriba' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 394 ../../../Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf/main.nf': 'arriba' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 399 Workflow-Corpus-Open-License/jianhong/universalModule + [10] Error in the file 'Workflow-Corpus-Open-License/jianhong/universalModule/chipseq.nf': Something went wrong in an include, possibly at line 14. No such file: 'Workflow-Corpus-Open-License/jianhong/universalModule/loadModule(checksum,.nf'. -- 400 ../../../Workflow-Corpus-Open-License/jianhong/universalModule - [10] Error in the file '../../../Workflow-Corpus-Open-License/jianhong/universalModule/chipseq.nf': Something went wrong in an include, possibly at line 14. No such file: '../../../Workflow-Corpus-Open-License/jianhong/universalModule/loadModule(checksum,.nf'. +- 413 Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline + [4] Error in the file 'Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline/subworkflow/SNV.nf': 'SNV' is trying to be created as a channel, possibly at line 27. It already exists as a process or a subworkflow in the nextflow file. -- 414 ../../../Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline - [4] Error in the file '../../../Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline/subworkflow/SNV.nf': 'SNV' is trying to be created as a channel, possibly at line 27. It already exists as a process or a subworkflow in the nextflow file. +- 418 Workflow-Corpus-Open-License/BrianLohman/cellranger-nf + [16] Error in the file 'Workflow-Corpus-Open-License/BrianLohman/cellranger-nf/main.nf': An odd number of '"""' was found in the code. -- 419 ../../../Workflow-Corpus-Open-License/BrianLohman/cellranger-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/BrianLohman/cellranger-nf/main.nf': An odd number of '"""' was found in the code. +- 427 Workflow-Corpus-Open-License/limrp/nextflow_subworkflow + [2] Error in the file 'Workflow-Corpus-Open-License/limrp/nextflow_subworkflow/subworkflows/local/fasta_metaprodigal_cdhit.nf': Not the same number of parameters given as input for the process 'PRODIGAL', possibly at line 21. -- 428 ../../../Workflow-Corpus-Open-License/limrp/nextflow_subworkflow - [2] Error in the file '../../../Workflow-Corpus-Open-License/limrp/nextflow_subworkflow/subworkflows/local/fasta_metaprodigal_cdhit.nf': Not the same number of parameters given as input for the process 'PRODIGAL', possibly at line 21. +- 428 Workflow-Corpus-Open-License/zajakin/sRNAflow + [16] Error in the file 'Workflow-Corpus-Open-License/zajakin/sRNAflow/sRNAflow.nf': No 'main' workflow was found. -- 429 ../../../Workflow-Corpus-Open-License/zajakin/sRNAflow - [16] Error in the file '../../../Workflow-Corpus-Open-License/zajakin/sRNAflow/sRNAflow.nf': No 'main' workflow was found. +- 435 Workflow-Corpus-Open-License/kullrich/snpless-nf + [4] Error in the file 'Workflow-Corpus-Open-License/kullrich/snpless-nf/main.nf': 'genmap' is trying to be created as a channel, possibly at line 263. It already exists as a process or a subworkflow in the nextflow file. -- 436 ../../../Workflow-Corpus-Open-License/kullrich/snpless-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/kullrich/snpless-nf/main.nf': 'genmap' is trying to be created as a channel, possibly at line 263. It already exists as a process or a subworkflow in the nextflow file. +- 436 Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel + [2] Error in the file 'Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel/flaq_amr_plus2.nf': Not the same number of parameters given as input for the process 'plusAnalyses'. -- 437 ../../../Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel - [2] Error in the file '../../../Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel/flaq_amr_plus2.nf': Not the same number of parameters given as input for the process 'plusAnalyses'. +- 443 Workflow-Corpus-Open-License/evotools/nSPECTRa + [4] Error in the file 'Workflow-Corpus-Open-License/evotools/nSPECTRa/include/workflow/mutyper.nf': 'chromosomeList' is trying to be created as a channel, possibly at line 10. It already exists as a process or a subworkflow in the nextflow file. -- 444 ../../../Workflow-Corpus-Open-License/evotools/nSPECTRa - [4] Error in the file '../../../Workflow-Corpus-Open-License/evotools/nSPECTRa/include/workflow/mutyper.nf': 'chromosomeList' is trying to be created as a channel, possibly at line 10. It already exists as a process or a subworkflow in the nextflow file. +- 444 Workflow-Corpus-Open-License/evotools/nf-LO + [18] Error in the file 'Workflow-Corpus-Open-License/evotools/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found. -- 445 ../../../Workflow-Corpus-Open-License/evotools/nf-LO - [18] Error in the file '../../../Workflow-Corpus-Open-License/evotools/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found. +- 448 Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf + [16] Error in the file 'Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf/main.nf': No 'main' workflow was found. -- 449 ../../../Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf/main.nf': No 'main' workflow was found. +- 449 Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf + [10] Error in the file 'Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/main.nf': Something went wrong in an include, possibly at line 68. No such file: 'Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/${subwork_folder}/tools.nf'. -- 450 ../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf - [10] Error in the file '../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/main.nf': Something went wrong in an include, possibly at line 68. No such file: '../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/${subwork_folder}/tools.nf'. +- 452 Workflow-Corpus-Open-License/palfalvi/rnaseq + [8] Error in the file 'Workflow-Corpus-Open-License/palfalvi/rnaseq/main.nf': The call for 'run_fastSE_qc' coudn't be found, before its use in the operation 'salmon_quantSE.out.collect().concat(run_fastSE_qc.out.collect())', possibly at line 217. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 453 ../../../Workflow-Corpus-Open-License/palfalvi/rnaseq - [8] Error in the file '../../../Workflow-Corpus-Open-License/palfalvi/rnaseq/main.nf': The call for 'run_fastSE_qc' coudn't be found, before its use in the operation 'salmon_quantSE.out.collect().concat(run_fastSE_qc.out.collect())', possibly at line 217. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 456 Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics + [16] Error in the file 'Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics/main.nf': No 'main' workflow was found. -- 457 ../../../Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics - [16] Error in the file '../../../Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics/main.nf': No 'main' workflow was found. +- 459 Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow + [4] Error in the file 'Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow/main.nf': 'PCA' is trying to be created as a channel, possibly at line 1. It already exists as a process or a subworkflow in the nextflow file. -- 460 ../../../Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow - [4] Error in the file '../../../Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow/main.nf': 'PCA' is trying to be created as a channel, possibly at line 1. It already exists as a process or a subworkflow in the nextflow file. +- 460 Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf + [2] Error in the file 'Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf/main.nf': Not the same number of parameters given as input for the process 'freebayes', possibly at line 159. -- 461 ../../../Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf - [2] Error in the file '../../../Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf/main.nf': Not the same number of parameters given as input for the process 'freebayes', possibly at line 159. +- 461 Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline + [18] Error in the file 'Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline/modules/messages.nf': 'startMessage' is expected to be defined in the file, but it could not be found. -- 462 ../../../Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline - [18] Error in the file '../../../Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline/modules/messages.nf': 'startMessage' is expected to be defined in the file, but it could not be found. +- 462 Workflow-Corpus-Open-License/mpieva/quicksand + [4] Error in the file 'Workflow-Corpus-Open-License/mpieva/quicksand/workflows/00_setup.nf': 'setup' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file. -- 463 ../../../Workflow-Corpus-Open-License/mpieva/quicksand - [4] Error in the file '../../../Workflow-Corpus-Open-License/mpieva/quicksand/workflows/00_setup.nf': 'setup' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file. +- 470 Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell + [2] Error in the file 'Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell/main.nf': Not the same number of parameters given as input for the process 'ENA_DOWNLOAD', possibly at line 123. -- 471 ../../../Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell - [2] Error in the file '../../../Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell/main.nf': Not the same number of parameters given as input for the process 'ENA_DOWNLOAD', possibly at line 123. +- 471 Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline + [16] Error in the file 'Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline/main.nf': No 'main' workflow was found. -- 472 ../../../Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline - [16] Error in the file '../../../Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline/main.nf': No 'main' workflow was found. +- 493 Workflow-Corpus-Open-License/RenzoTale88/nf-LO + [18] Error in the file 'Workflow-Corpus-Open-License/RenzoTale88/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found. -- 494 ../../../Workflow-Corpus-Open-License/RenzoTale88/nf-LO - [18] Error in the file '../../../Workflow-Corpus-Open-License/RenzoTale88/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found. +- 495 Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek + [22] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek/subworkflows/local/preprocessing_read_qc.nf': Multiple 'emit:' were found in the subworkflow 'PREPROCESSING_READ_QC'. -- 496 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek - [22] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek/subworkflows/local/preprocessing_read_qc.nf': Multiple 'emit:' were found in the subworkflow 'PREPROCESSING_READ_QC'. +- 497 Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret + [4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret/subworkflows/msa.nf': 'msa' is trying to be created as a channel, possibly at line 7. It already exists as a process or a subworkflow in the nextflow file. -- 498 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret - [4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret/subworkflows/msa.nf': 'msa' is trying to be created as a channel, possibly at line 7. It already exists as a process or a subworkflow in the nextflow file. +- 498 Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls + [4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls/workflows/assembly.nf': 'assembly' is trying to be created as a channel, possibly at line 11. It already exists as a process or a subworkflow in the nextflow file. -- 499 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls - [4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls/workflows/assembly.nf': 'assembly' is trying to be created as a channel, possibly at line 11. It already exists as a process or a subworkflow in the nextflow file. +- 499 Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur + [4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur/subworkflows/average_nucleotide_identity.nf': 'datasets_summary' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file. -- 500 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur - [4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur/subworkflows/average_nucleotide_identity.nf': 'datasets_summary' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file. +- 504 Workflow-Corpus-Open-License/ikmb/nf-template + [2] Error in the file 'Workflow-Corpus-Open-License/ikmb/nf-template/main.nf': Not the same number of parameters given as input for the subworklfow 'MAIN' in the call, possibly at line 38. -- 505 ../../../Workflow-Corpus-Open-License/ikmb/nf-template - [2] Error in the file '../../../Workflow-Corpus-Open-License/ikmb/nf-template/main.nf': Not the same number of parameters given as input for the subworklfow 'MAIN' in the call, possibly at line 38. +- 509 Workflow-Corpus-Open-License/h3abionet/TADA + [22] Error in the file 'Workflow-Corpus-Open-License/h3abionet/TADA/main.nf': Multiple 'when:' were found in the process 'ToQIIME2Aln'. -- 510 ../../../Workflow-Corpus-Open-License/h3abionet/TADA - [22] Error in the file '../../../Workflow-Corpus-Open-License/h3abionet/TADA/main.nf': Multiple 'when:' were found in the process 'ToQIIME2Aln'. +- 515 Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns + [8] Error in the file 'Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns/emit_example.nf': The call for 'doo_foo' coudn't be found, before its use in the operation 'doo_foo.out.foo_item', possibly at line 44. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 516 ../../../Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns - [8] Error in the file '../../../Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns/emit_example.nf': The call for 'doo_foo' coudn't be found, before its use in the operation 'doo_foo.out.foo_item', possibly at line 44. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 518 Workflow-Corpus-Open-License/guigolab/FA-nf + [16] Error in the file 'Workflow-Corpus-Open-License/guigolab/FA-nf/main.nf': Not the same number of opening and closing parentheses '()' in the file. -- 519 ../../../Workflow-Corpus-Open-License/guigolab/FA-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/FA-nf/main.nf': Not the same number of opening and closing parentheses '()' in the file. +- 521 Workflow-Corpus-Open-License/guigolab/geneidx + [10] Error in the file 'Workflow-Corpus-Open-License/guigolab/geneidx/main.nf': Something went wrong in an include, possibly at line 34. No such file: 'Workflow-Corpus-Open-License/guigolab/geneidx/${wk_folder}/GENEIDX.nf'. -- 522 ../../../Workflow-Corpus-Open-License/guigolab/geneidx - [10] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/geneidx/main.nf': Something went wrong in an include, possibly at line 34. No such file: '../../../Workflow-Corpus-Open-License/guigolab/geneidx/${wk_folder}/GENEIDX.nf'. +- 522 Workflow-Corpus-Open-License/guigolab/ipsa-nf + [4] Error in the file 'Workflow-Corpus-Open-License/guigolab/ipsa-nf/ipsa.nf': 'ssjA06' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 523 ../../../Workflow-Corpus-Open-License/guigolab/ipsa-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/ipsa-nf/ipsa.nf': 'ssjA06' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 526 Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline + [10] Error in the file 'Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/subworkflows/local/input_check.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/modules/local/samplesheet_check.nf'. -- 527 ../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline - [10] Error in the file '../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/subworkflows/local/input_check.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/modules/local/samplesheet_check.nf'. - -- 541 ../../../Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc - [14] Error in the file '../../../Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc/subworkflows/local/tidk.nf': 'set { ch_list_of_a_posteriori_tidk_plots }' is neither a process, subworkflow or an operator. In the executor 'ch_explored_repeat_seq +- 540 Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc + [14] Error in the file 'Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc/subworkflows/local/tidk.nf': 'set { ch_list_of_a_posteriori_tidk_plots }' is neither a process, subworkflow or an operator. In the executor 'ch_explored_repeat_seq .join( ch_sorted_hap_file ) @@ -369,42 +366,42 @@ | collect | set { ch_list_of_a_posteriori_tidk_plots }', possibly at line 18. -- 545 ../../../Workflow-Corpus-Open-License/nf-core/raredisease - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/raredisease/workflows/raredisease.nf': To much to unpack : The subworkflow 'PREPARE_REFERENCES' emits over one channel in a operation, possibly at line 164. +- 544 Workflow-Corpus-Open-License/nf-core/raredisease + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/raredisease/workflows/raredisease.nf': To much to unpack : The subworkflow 'PREPARE_REFERENCES' emits over one channel in a operation, possibly at line 164. -- 549 ../../../Workflow-Corpus-Open-License/nf-core/genomeannotator - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/genomeannotator/workflows/genomeannotator.nf': The call for 'AUGUSTUS_TRAINING' coudn't be found, before its use in the operation 'ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder', possibly at line 293. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 548 Workflow-Corpus-Open-License/nf-core/genomeannotator + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/genomeannotator/workflows/genomeannotator.nf': The call for 'AUGUSTUS_TRAINING' coudn't be found, before its use in the operation 'ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder', possibly at line 293. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 550 ../../../Workflow-Corpus-Open-License/nf-core/circrna - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/circrna/workflows/circrna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 115. +- 549 Workflow-Corpus-Open-License/nf-core/circrna + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/circrna/workflows/circrna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 115. -- 551 ../../../Workflow-Corpus-Open-License/nf-core/ampliseq - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/ampliseq/workflows/ampliseq.nf': To much to unpack : The subworkflow 'CUTADAPT_WORKFLOW' emits over one channel in a operation, possibly at line 323. +- 550 Workflow-Corpus-Open-License/nf-core/ampliseq + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/ampliseq/workflows/ampliseq.nf': To much to unpack : The subworkflow 'CUTADAPT_WORKFLOW' emits over one channel in a operation, possibly at line 323. -- 552 ../../../Workflow-Corpus-Open-License/nf-core/readsimulator - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/readsimulator/workflows/readsimulator/main.nf': The call for 'MERGE_FASTAS' coudn't be found, before its use in the operation 'ch_fasta = MERGE_FASTAS.out.fasta +- 551 Workflow-Corpus-Open-License/nf-core/readsimulator + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/readsimulator/workflows/readsimulator/main.nf': The call for 'MERGE_FASTAS' coudn't be found, before its use in the operation 'ch_fasta = MERGE_FASTAS.out.fasta .map { meta, fasta -> return fasta }', possibly at line 109. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 553 ../../../Workflow-Corpus-Open-License/nf-core/chipseq - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/chipseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 177. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 552 Workflow-Corpus-Open-License/nf-core/chipseq + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/chipseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 177. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 554 ../../../Workflow-Corpus-Open-License/nf-core/crisprseq - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/crisprseq/workflows/crisprseq_targeted.nf': Tried to access the emit 'PREPROCESSING_SUMMARY.out.versions' but the Process 'PREPROCESSING_SUMMARY' has not been called in the subworkflow 'CRISPRSEQ_TARGETED'. +- 553 Workflow-Corpus-Open-License/nf-core/crisprseq + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/crisprseq/workflows/crisprseq_targeted.nf': Tried to access the emit 'PREPROCESSING_SUMMARY.out.versions' but the Process 'PREPROCESSING_SUMMARY' has not been called in the subworkflow 'CRISPRSEQ_TARGETED'. -- 555 ../../../Workflow-Corpus-Open-License/nf-core/rnafusion - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnafusion/workflows/rnafusion.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 126. +- 554 Workflow-Corpus-Open-License/nf-core/rnafusion + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnafusion/workflows/rnafusion.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 126. -- 559 ../../../Workflow-Corpus-Open-License/nf-core/mag - [2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/mag/subworkflows/local/binning.nf': Not the same number of parameters given as input for the subworklfow 'FASTA_BINNING_CONCOCT' in the call, possibly at line 97. +- 558 Workflow-Corpus-Open-License/nf-core/mag + [2] Error in the file 'Workflow-Corpus-Open-License/nf-core/mag/subworkflows/local/binning.nf': Not the same number of parameters given as input for the subworklfow 'FASTA_BINNING_CONCOCT' in the call, possibly at line 97. -- 564 ../../../Workflow-Corpus-Open-License/nf-core/mhcquant - [22] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/mhcquant/modules/local/samplesheet_check.nf': Multiple 'when:' were found in the process 'SAMPLESHEET_CHECK'. +- 563 Workflow-Corpus-Open-License/nf-core/mhcquant + [22] Error in the file 'Workflow-Corpus-Open-License/nf-core/mhcquant/modules/local/samplesheet_check.nf': Multiple 'when:' were found in the process 'SAMPLESHEET_CHECK'. -- 565 ../../../Workflow-Corpus-Open-License/nf-core/airrflow - [14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/airrflow/subworkflows/local/assembled_input_check.nf': 'fa]$/ +- 564 Workflow-Corpus-Open-License/nf-core/airrflow + [14] Error in the file 'Workflow-Corpus-Open-License/nf-core/airrflow/subworkflows/local/assembled_input_check.nf': 'fa]$/ tsv: it[0].filename =~ /tsv$/ } .set{ ch_metadata }' is neither a process, subworkflow or an operator. In the executor 'ch_validated_input @@ -416,123 +413,123 @@ } .set{ ch_metadata }', possibly at line 21. -- 567 ../../../Workflow-Corpus-Open-License/nf-core/rnasplice - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnasplice/workflows/rnasplice.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 161. +- 566 Workflow-Corpus-Open-License/nf-core/rnasplice + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnasplice/workflows/rnasplice.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 161. -- 569 ../../../Workflow-Corpus-Open-License/nf-core/demultiplex - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/demultiplex/workflows/demultiplex.nf': Tried to access the emit 'UNTAR.out.versions' but the Process 'UNTAR' has not been called in the subworkflow 'DEMULTIPLEX'. +- 568 Workflow-Corpus-Open-License/nf-core/demultiplex + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/demultiplex/workflows/demultiplex.nf': Tried to access the emit 'UNTAR.out.versions' but the Process 'UNTAR' has not been called in the subworkflow 'DEMULTIPLEX'. -- 572 ../../../Workflow-Corpus-Open-License/nf-core/smrnaseq - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/smrnaseq/workflows/smrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 104. +- 571 Workflow-Corpus-Open-License/nf-core/smrnaseq + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/smrnaseq/workflows/smrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 104. -- 573 ../../../Workflow-Corpus-Open-License/nf-core/dualrnaseq - [4] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/dualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 572 Workflow-Corpus-Open-License/nf-core/dualrnaseq + [4] Error in the file 'Workflow-Corpus-Open-License/nf-core/dualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 574 ../../../Workflow-Corpus-Open-License/nf-core/nascent - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/nascent/subworkflows/local/prepare_genome.nf': The call for 'UNTAR_DRAGMAP_INDEX' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)', possibly at line 122. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 573 Workflow-Corpus-Open-License/nf-core/nascent + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/nascent/subworkflows/local/prepare_genome.nf': The call for 'UNTAR_DRAGMAP_INDEX' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)', possibly at line 122. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 577 ../../../Workflow-Corpus-Open-License/nf-core/configs - [16] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/configs/configtest.nf': No 'main' workflow was found. +- 576 Workflow-Corpus-Open-License/nf-core/configs + [16] Error in the file 'Workflow-Corpus-Open-License/nf-core/configs/configtest.nf': No 'main' workflow was found. -- 579 ../../../Workflow-Corpus-Open-License/nf-core/modules - [16] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/modules/main.nf': No 'main' workflow was found. +- 578 Workflow-Corpus-Open-License/nf-core/modules + [16] Error in the file 'Workflow-Corpus-Open-License/nf-core/modules/main.nf': No 'main' workflow was found. -- 581 ../../../Workflow-Corpus-Open-License/nf-core/ssds - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/ssds/subworkflows/local/sort_and_index_bam.nf': The call for 'SAMTOOLS_SORTSAM' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SAMTOOLS_SORTSAM.out.versions.first())', possibly at line 17. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 580 Workflow-Corpus-Open-License/nf-core/ssds + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/ssds/subworkflows/local/sort_and_index_bam.nf': The call for 'SAMTOOLS_SORTSAM' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SAMTOOLS_SORTSAM.out.versions.first())', possibly at line 17. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 583 ../../../Workflow-Corpus-Open-License/nf-core/phageannotator - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/phageannotator/workflows/phageannotator/main.nf': To much to unpack : The subworkflow 'FASTQ_VIRUS_ENRICHMENT_VIROMEQC' emits over one channel in a operation, possibly at line 78. +- 582 Workflow-Corpus-Open-License/nf-core/phageannotator + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/phageannotator/workflows/phageannotator/main.nf': To much to unpack : The subworkflow 'FASTQ_VIRUS_ENRICHMENT_VIROMEQC' emits over one channel in a operation, possibly at line 78. -- 585 ../../../Workflow-Corpus-Open-License/nf-core/metaboigniter - [14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/metaboigniter/subworkflows/local/mergems1ms2.nf': 'OPENMS_FILEMERGER' is neither a process, subworkflow or an operator. In the executor 'mzml_files.filter{meta,file->meta.level != "MS2"}.combine(OPENMS_FILEFILTERMS2.out.mzml.map{it[1]}).groupTuple(by:[0,1]) | OPENMS_FILEMERGER', possibly at line 19. +- 584 Workflow-Corpus-Open-License/nf-core/metaboigniter + [14] Error in the file 'Workflow-Corpus-Open-License/nf-core/metaboigniter/subworkflows/local/mergems1ms2.nf': 'OPENMS_FILEMERGER' is neither a process, subworkflow or an operator. In the executor 'mzml_files.filter{meta,file->meta.level != "MS2"}.combine(OPENMS_FILEFILTERMS2.out.mzml.map{it[1]}).groupTuple(by:[0,1]) | OPENMS_FILEMERGER', possibly at line 19. -- 586 ../../../Workflow-Corpus-Open-License/nf-core/epitopeprediction - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/epitopeprediction/workflows/epitopeprediction.nf': The call for 'SHOW_SUPPORTED_MODELS' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SHOW_SUPPORTED_MODELS.out.versions.ifEmpty(null))', possibly at line 180. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 585 Workflow-Corpus-Open-License/nf-core/epitopeprediction + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/epitopeprediction/workflows/epitopeprediction.nf': The call for 'SHOW_SUPPORTED_MODELS' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SHOW_SUPPORTED_MODELS.out.versions.ifEmpty(null))', possibly at line 180. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 590 ../../../Workflow-Corpus-Open-License/nf-core/genomeassembler - [2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/genomeassembler/subworkflows/local/evaluate_gene_space.nf': Not the same number of parameters given as input for the process 'BUSCO', possibly at line 10. +- 589 Workflow-Corpus-Open-License/nf-core/genomeassembler + [2] Error in the file 'Workflow-Corpus-Open-License/nf-core/genomeassembler/subworkflows/local/evaluate_gene_space.nf': Not the same number of parameters given as input for the process 'BUSCO', possibly at line 10. -- 591 ../../../Workflow-Corpus-Open-License/nf-core/circdna - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/circdna/workflows/circdna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 190. +- 590 Workflow-Corpus-Open-License/nf-core/circdna + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/circdna/workflows/circdna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 190. -- 592 ../../../Workflow-Corpus-Open-License/nf-core/fetchngs - [2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/fetchngs/main.nf': Not the same number of parameters given as input for the subworklfow 'SYNAPSE' in the call, possibly at line 46. +- 591 Workflow-Corpus-Open-License/nf-core/fetchngs + [2] Error in the file 'Workflow-Corpus-Open-License/nf-core/fetchngs/main.nf': Not the same number of parameters given as input for the subworklfow 'SYNAPSE' in the call, possibly at line 46. -- 593 ../../../Workflow-Corpus-Open-License/nf-core/multiplesequencealign - [22] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/multiplesequencealign/modules/local/prepare_shiny.nf': Multiple 'when:' were found in the process 'PREPARE_SHINY'. +- 592 Workflow-Corpus-Open-License/nf-core/multiplesequencealign + [22] Error in the file 'Workflow-Corpus-Open-License/nf-core/multiplesequencealign/modules/local/prepare_shiny.nf': Multiple 'when:' were found in the process 'PREPARE_SHINY'. -- 597 ../../../Workflow-Corpus-Open-License/nf-core/taxprofiler - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/taxprofiler/subworkflows/local/shortread_preprocessing.nf': To much to unpack : The subworkflow 'SHORTREAD_FASTP' emits over one channel in a operation, possibly at line 21. +- 596 Workflow-Corpus-Open-License/nf-core/taxprofiler + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/taxprofiler/subworkflows/local/shortread_preprocessing.nf': To much to unpack : The subworkflow 'SHORTREAD_FASTP' emits over one channel in a operation, possibly at line 21. -- 598 ../../../Workflow-Corpus-Open-License/nf-core/metatdenovo - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/metatdenovo/workflows/metatdenovo.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 146. +- 597 Workflow-Corpus-Open-License/nf-core/metatdenovo + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/metatdenovo/workflows/metatdenovo.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 146. -- 599 ../../../Workflow-Corpus-Open-License/nf-core/viralrecon - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/viralrecon/workflows/illumina.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 163. +- 598 Workflow-Corpus-Open-License/nf-core/viralrecon + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/viralrecon/workflows/illumina.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 163. -- 600 ../../../Workflow-Corpus-Open-License/nf-core/scrnaseq - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/scrnaseq/workflows/scrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 121. +- 599 Workflow-Corpus-Open-License/nf-core/scrnaseq + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/scrnaseq/workflows/scrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 121. -- 602 ../../../Workflow-Corpus-Open-License/nf-core/rnadnavar - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnadnavar/subworkflows/local/prepare_genome/main.nf': The call for 'GUNZIP_GFF' coudn't be found, before its use in the operation 'ch_gff = GUNZIP_GFF.out.gunzip.map{ meta, gff -> [gff] }.collect()', possibly at line 98. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 601 Workflow-Corpus-Open-License/nf-core/rnadnavar + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnadnavar/subworkflows/local/prepare_genome/main.nf': The call for 'GUNZIP_GFF' coudn't be found, before its use in the operation 'ch_gff = GUNZIP_GFF.out.gunzip.map{ meta, gff -> [gff] }.collect()', possibly at line 98. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 606 ../../../Workflow-Corpus-Open-License/nf-core/rnavar - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnavar/workflows/rnavar.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 138. +- 605 Workflow-Corpus-Open-License/nf-core/rnavar + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnavar/workflows/rnavar.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 138. -- 610 ../../../Workflow-Corpus-Open-License/nf-core/nanoseq - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/nanoseq/subworkflows/local/rna_modifications_xpore_m6anet.nf': Tried to access the emit 'NANOPOLISH_INDEX_EVENTALIGN.out.nanopolish_outputs' but the Process 'NANOPOLISH_INDEX_EVENTALIGN' has not been called in the subworkflow 'RNA_MODIFICATION_XPORE_M6ANET'. +- 609 Workflow-Corpus-Open-License/nf-core/nanoseq + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/nanoseq/subworkflows/local/rna_modifications_xpore_m6anet.nf': Tried to access the emit 'NANOPOLISH_INDEX_EVENTALIGN.out.nanopolish_outputs' but the Process 'NANOPOLISH_INDEX_EVENTALIGN' has not been called in the subworkflow 'RNA_MODIFICATION_XPORE_M6ANET'. -- 612 ../../../Workflow-Corpus-Open-License/nf-core/radseq - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/radseq/workflows/radseq.nf': To much to unpack : The subworkflow 'CDHIT_RAINBOW' emits over one channel in a operation, possibly at line 97. +- 611 Workflow-Corpus-Open-License/nf-core/radseq + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/radseq/workflows/radseq.nf': To much to unpack : The subworkflow 'CDHIT_RAINBOW' emits over one channel in a operation, possibly at line 97. -- 613 ../../../Workflow-Corpus-Open-License/nf-core/atacseq - [8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/atacseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 199. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. +- 612 Workflow-Corpus-Open-License/nf-core/atacseq + [8] Error in the file 'Workflow-Corpus-Open-License/nf-core/atacseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 199. Either because the call wasn't made before the operation or that the element it is calling doesn't exist. -- 614 ../../../Workflow-Corpus-Open-License/nf-core/proteinfold - [20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/proteinfold/workflows/alphafold2.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 81. +- 613 Workflow-Corpus-Open-License/nf-core/proteinfold + [20] Error in the file 'Workflow-Corpus-Open-License/nf-core/proteinfold/workflows/alphafold2.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 81. -- 620 ../../../Workflow-Corpus-Open-License/nf-core/quantms - [14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/quantms/workflows/quantms.nf': 'set {ch_db_for_decoy_creation_or_null}' is neither a process, subworkflow or an operator. In the executor 'CREATE_INPUT_CHANNEL.out.ch_meta_config_iso.mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq).first() +- 619 Workflow-Corpus-Open-License/nf-core/quantms + [14] Error in the file 'Workflow-Corpus-Open-License/nf-core/quantms/workflows/quantms.nf': 'set {ch_db_for_decoy_creation_or_null}' is neither a process, subworkflow or an operator. In the executor 'CREATE_INPUT_CHANNEL.out.ch_meta_config_iso.mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq).first() | combine( ch_db_for_decoy_creation ) | map { it[-1] } | set {ch_db_for_decoy_creation_or_null}', possibly at line 135. -- 623 ../../../Workflow-Corpus-Open-License/lisemangiante/test_nextflow - [4] Error in the file '../../../Workflow-Corpus-Open-License/lisemangiante/test_nextflow/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file. +- 622 Workflow-Corpus-Open-License/lisemangiante/test_nextflow + [4] Error in the file 'Workflow-Corpus-Open-License/lisemangiante/test_nextflow/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file. -- 635 ../../../Workflow-Corpus-Open-License/matsengrp/phip-flow - [14] Error in the file '../../../Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf': In the executor 'ds | to_csv | run_edgeR | run_BEER | (append_assay_csvs_to_xarray & publish_rds)', '(append_assay_csvs_to_xarray & publish_rds)' is neither a process, subworkflow or an operator (in the file '../../../Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf') +- 634 Workflow-Corpus-Open-License/matsengrp/phip-flow + [14] Error in the file 'Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf': In the executor 'ds | to_csv | run_edgeR | run_BEER | (append_assay_csvs_to_xarray & publish_rds)', '(append_assay_csvs_to_xarray & publish_rds)' is neither a process, subworkflow or an operator (in the file 'Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf') -- 644 ../../../Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf/modules.nf': No 'main' workflow was found. +- 643 Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf + [16] Error in the file 'Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf/modules.nf': No 'main' workflow was found. -- 645 ../../../Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem - [20] Error in the file '../../../Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem/workflows/resequencing-mem.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 67. +- 644 Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem + [20] Error in the file 'Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem/workflows/resequencing-mem.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 67. -- 647 ../../../Workflow-Corpus-Open-License/alam1988/Nextflow - [12] Error in the file '../../../Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf': An include ('include { SRA_DOWNLOAD } from './sra_download'') was found in the main in the file '../../../Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf'. FlowInsight does not support this -> see specification list. +- 646 Workflow-Corpus-Open-License/alam1988/Nextflow + [12] Error in the file 'Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf': An include ('include { SRA_DOWNLOAD } from './sra_download'') was found in the main in the file 'Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf'. FlowInsight does not support this -> see specification list. -- 650 ../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf - [22] Error in the file '../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf/hybpiper.nf': Multiple 'take:' were found in the subworkflow 'fix_targetfile_main'. +- 649 Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf + [22] Error in the file 'Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf/hybpiper.nf': Multiple 'take:' were found in the subworkflow 'fix_targetfile_main'. -- 658 ../../../Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB - [16] Error in the file '../../../Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB/main.nf': No 'main' workflow was found. +- 657 Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB + [16] Error in the file 'Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB/main.nf': No 'main' workflow was found. -- 659 ../../../Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow - [6] Error in the file '../../../Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow/modules/bowtieMapping.nf': One channel was expected in the emit 'makeIndex.out'. Even though multiple emits are defined for the workflow 'makeIndex' +- 658 Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow + [6] Error in the file 'Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow/modules/bowtieMapping.nf': One channel was expected in the emit 'makeIndex.out'. Even though multiple emits are defined for the workflow 'makeIndex' -- 663 ../../../Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf - [16] Error in the file '../../../Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf/main.nf': No 'main' workflow was found. +- 662 Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf + [16] Error in the file 'Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf/main.nf': No 'main' workflow was found. -- 670 ../../../Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq - [4] Error in the file '../../../Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 669 Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq + [4] Error in the file 'Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 672 ../../../Workflow-Corpus-Open-License/msk-mind/clam-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/msk-mind/clam-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 671 Workflow-Corpus-Open-License/msk-mind/clam-nf + [4] Error in the file 'Workflow-Corpus-Open-License/msk-mind/clam-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 673 ../../../Workflow-Corpus-Open-License/msk-mind/oncofusion-nf - [4] Error in the file '../../../Workflow-Corpus-Open-License/msk-mind/oncofusion-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. +- 672 Workflow-Corpus-Open-License/msk-mind/oncofusion-nf + [4] Error in the file 'Workflow-Corpus-Open-License/msk-mind/oncofusion-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file. -- 675 ../../../Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline - [16] Error in the file '../../../Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline/main.nf': No 'main' workflow was found. +- 674 Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline + [16] Error in the file 'Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline/main.nf': No 'main' workflow was found. diff --git a/github-crawler b/github-crawler deleted file mode 160000 index bf6322002948c7b3df3657e0bd0e5fd82e7c8bd5..0000000000000000000000000000000000000000 --- a/github-crawler +++ /dev/null @@ -1 +0,0 @@ -Subproject commit bf6322002948c7b3df3657e0bd0e5fd82e7c8bd5 diff --git a/study.ipynb b/study.ipynb index 1e6b469406f86c6ceb39160f6c92a44298958107..011f2115b08d0370ccdb74709cc70b53e894d134 100644 --- a/study.ipynb +++ b/study.ipynb @@ -38,9 +38,6 @@ "import re\n", "\n", "current_path= os.getcwd()\n", - "os.chdir(\"github-crawler/\")\n", - "from download_corpus import download\n", - "os.chdir(current_path)\n", "\n", "os.chdir(\"bioflow-insight/\")\n", "from src.nextflow_file import Nextflow_File\n", @@ -81,8 +78,6 @@ "source": [ "#Bool to download workflow\n", "download_files = False\n", - "#Path to folder containing workflows (where they will also be downloaded)\n", - "path_2_workflows = \"../../../Workflow-Corpus-Open-License\"\n", "#Bool to run analysis ~6minutes on a 13th Gen Intel® Core™ i5-1335U × 12 (32gb of ram)\n", "run_analysis_on_corpus = True\n", "#Bool to analyse the results\n", @@ -102,14 +97,10 @@ "metadata": {}, "outputs": [], "source": [ - "#Read crawler results\n", - "with open(\"./github-crawler/wf_crawl_nextflow.json\") as json_file:\n", - " crawler = json.load(json_file)\n", - "_ = crawler.pop(\"last_date\")\n", - "\n", "#Downloading the files\n", "if(download_files):\n", - " download(path_2_workflows, crawler)" + " os.system('wget https://zenodo.org/records/10817606/files/BioFlow-Insight-Workflow-Corpus-Open-License.zip')\n", + " os.system('unzip BioFlow-Insight-Workflow-Corpus-Open-License.zip')" ] }, { @@ -128,12 +119,12 @@ "name": "stdout", "output_type": "stream", "text": [ - "In total there are 678 workflows.\n" + "In total there are 677 workflows.\n" ] } ], "source": [ - "workflows = glob.glob(f'{path_2_workflows}/*/*', recursive=False)\n", + "workflows = glob.glob(f'Workflow-Corpus-Open-License/*/*', recursive=False)\n", "\n", "print(f\"In total there are {len(workflows)} workflows.\")" ] @@ -147,678 +138,676 @@ "name": "stdout", "output_type": "stream", "text": [ - "0 ../../../Workflow-Corpus-Open-License/KevinMenden/hybrid-assembly\n", - "1 ../../../Workflow-Corpus-Open-License/ezorita/chip-nf\n", - "2 ../../../Workflow-Corpus-Open-License/GiantSpaceRobot/tsRNAsearch\n", - "3 ../../../Workflow-Corpus-Open-License/ctmrbio/BACTpipe\n", - "4 ../../../Workflow-Corpus-Open-License/wtsi-hgi/nf_cellbender\n", - "5 ../../../Workflow-Corpus-Open-License/grbot/run-fastqc\n", - "6 ../../../Workflow-Corpus-Open-License/grbot/nextflow-hack17-tutorial\n", - "7 ../../../Workflow-Corpus-Open-License/hunglin59638/plott\n", - "8 ../../../Workflow-Corpus-Open-License/codingene/nextflow-base\n", - "9 ../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/nf-iap.nf': Something went wrong in an include, possibly at line 88. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/NextflowModules/Utils/fastq.nf'.\n", - "10 ../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/WGS.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/NextflowModules/Utils/fastq.nf'.\n", - "11 ../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/WES_Fingerprint.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/NextflowModules/Utils/bam.nf'.\n", - "12 ../../../Workflow-Corpus-Open-License/Aveglia/vAMPirus\n", - "13 ../../../Workflow-Corpus-Open-License/telatin/cleanup\n", - "14 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/nf-methylpy\n", - "15 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/kWIP-nf\n", - "16 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis\n", - "[3] Error in the file '../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis/workflows/aradeepopsis.nf': Don't know how to handle '( params.masks ? MASKS : SEGMENT )' in a pipe operator, possibly at line 56. Try using the recommended operator composition.\n", - "17 ../../../Workflow-Corpus-Open-License/marcodelapierre/trinity-nf\n", - "18 ../../../Workflow-Corpus-Open-License/marcodelapierre/toy-gpu-nf\n", - "19 ../../../Workflow-Corpus-Open-License/marcodelapierre/nanopore-nf\n", - "20 ../../../Workflow-Corpus-Open-License/marcodelapierre/hello-nextflow\n", - "21 ../../../Workflow-Corpus-Open-License/marcodelapierre/illumina-nf\n", - "22 ../../../Workflow-Corpus-Open-License/maxemil/ALE-pipeline\n", - "23 ../../../Workflow-Corpus-Open-License/maxemil/Biodiversity-pipeline\n", - "24 ../../../Workflow-Corpus-Open-License/brwnj/smoove-nf\n", - "[5] Error in the file '../../../Workflow-Corpus-Open-License/brwnj/smoove-nf/main.nf': A ternary conditional operator was used with an tuple, possibly at line 297. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way.\n", - "25 ../../../Workflow-Corpus-Open-License/brwnj/facets-nf\n", - "26 ../../../Workflow-Corpus-Open-License/brwnj/covviz\n", - "[5] Error in the file '../../../Workflow-Corpus-Open-License/brwnj/covviz/main.nf': A ternary conditional operator was used with an tuple, possibly at line 125. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way.\n", - "27 ../../../Workflow-Corpus-Open-License/brwnj/idplot\n", - "28 ../../../Workflow-Corpus-Open-License/phc-health/nextflow-pangolin\n", - "29 ../../../Workflow-Corpus-Open-License/phipsonlab/NextClone\n", - "30 ../../../Workflow-Corpus-Open-License/SFGLab/ConsensuSV-nf-pipeline\n", - "31 ../../../Workflow-Corpus-Open-License/canceromics/MeRIPseqPipe\n", - "32 ../../../Workflow-Corpus-Open-License/AustralianBioCommons/Nextflow_DSL2_template\n", - "33 ../../../Workflow-Corpus-Open-License/AustralianBioCommons/hifi-assembly-workflow\n", - "34 ../../../Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen/workflows/bacterial_base.nf': 'quast' is trying to be created as a channel, possibly at line 16. It already exists as a process or a subworkflow in the nextflow file.\n", - "35 ../../../Workflow-Corpus-Open-License/stracquadaniolab/cubseq-nf\n", - "36 ../../../Workflow-Corpus-Open-License/stracquadaniolab/quick-rnaseq-nf\n", - "37 ../../../Workflow-Corpus-Open-License/APHA-CSU/hello-nextflow\n", - "38 ../../../Workflow-Corpus-Open-License/eipm/hello-mess-nf\n", - "39 ../../../Workflow-Corpus-Open-License/amchakra/tosca\n", - "40 ../../../Workflow-Corpus-Open-License/ksumngs/v-met\n", - "41 ../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline/workflows/cmgg-germline.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 250.\n", - "42 ../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural/workflows/cmgg-structural.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 135.\n", - "43 ../../../Workflow-Corpus-Open-License/gerlichlab/scshic_pipeline\n", - "44 ../../../Workflow-Corpus-Open-License/pblaney/mgp1000\n", - "45 ../../../Workflow-Corpus-Open-License/Midnighter/nextflow-utility-services\n", - "46 ../../../Workflow-Corpus-Open-License/Midnighter/nf-slack\n", - "47 ../../../Workflow-Corpus-Open-License/jnoms/virID\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/jnoms/virID/virID.nf': 'bwa_mem_contigs' is neither a process, subworkflow or an operator. In the executor 'contigs\n", + "0 Workflow-Corpus-Open-License/KevinMenden/hybrid-assembly\n", + "1 Workflow-Corpus-Open-License/ezorita/chip-nf\n", + "2 Workflow-Corpus-Open-License/GiantSpaceRobot/tsRNAsearch\n", + "3 Workflow-Corpus-Open-License/ctmrbio/BACTpipe\n", + "4 Workflow-Corpus-Open-License/wtsi-hgi/nf_cellbender\n", + "5 Workflow-Corpus-Open-License/grbot/run-fastqc\n", + "6 Workflow-Corpus-Open-License/grbot/nextflow-hack17-tutorial\n", + "7 Workflow-Corpus-Open-License/hunglin59638/plott\n", + "8 Workflow-Corpus-Open-License/codingene/nextflow-base\n", + "9 Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/nf-iap.nf': Something went wrong in an include, possibly at line 88. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/NF-IAP/NextflowModules/Utils/fastq.nf'.\n", + "10 Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/WGS.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWGS/NextflowModules/Utils/fastq.nf'.\n", + "11 Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/WES_Fingerprint.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/UMCUGenetics/DxNextflowWES/NextflowModules/Utils/bam.nf'.\n", + "12 Workflow-Corpus-Open-License/Aveglia/vAMPirus\n", + "13 Workflow-Corpus-Open-License/telatin/cleanup\n", + "14 Workflow-Corpus-Open-License/Gregor-Mendel-Institute/nf-methylpy\n", + "15 Workflow-Corpus-Open-License/Gregor-Mendel-Institute/kWIP-nf\n", + "16 Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis\n", + "[3] Error in the file 'Workflow-Corpus-Open-License/Gregor-Mendel-Institute/aradeepopsis/workflows/aradeepopsis.nf': Don't know how to handle '( params.masks ? MASKS : SEGMENT )' in a pipe operator, possibly at line 56. Try using the recommended operator composition.\n", + "17 Workflow-Corpus-Open-License/marcodelapierre/trinity-nf\n", + "18 Workflow-Corpus-Open-License/marcodelapierre/toy-gpu-nf\n", + "19 Workflow-Corpus-Open-License/marcodelapierre/nanopore-nf\n", + "20 Workflow-Corpus-Open-License/marcodelapierre/hello-nextflow\n", + "21 Workflow-Corpus-Open-License/marcodelapierre/illumina-nf\n", + "22 Workflow-Corpus-Open-License/maxemil/ALE-pipeline\n", + "23 Workflow-Corpus-Open-License/maxemil/Biodiversity-pipeline\n", + "24 Workflow-Corpus-Open-License/brwnj/smoove-nf\n", + "[5] Error in the file 'Workflow-Corpus-Open-License/brwnj/smoove-nf/main.nf': A ternary conditional operator was used with an tuple, possibly at line 297. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way.\n", + "25 Workflow-Corpus-Open-License/brwnj/facets-nf\n", + "26 Workflow-Corpus-Open-License/brwnj/covviz\n", + "[5] Error in the file 'Workflow-Corpus-Open-License/brwnj/covviz/main.nf': A ternary conditional operator was used with an tuple, possibly at line 125. BioFlow-Insight doesn't support this yet (see specification list), try defining the operation in a different way.\n", + "27 Workflow-Corpus-Open-License/brwnj/idplot\n", + "28 Workflow-Corpus-Open-License/phc-health/nextflow-pangolin\n", + "29 Workflow-Corpus-Open-License/phipsonlab/NextClone\n", + "30 Workflow-Corpus-Open-License/SFGLab/ConsensuSV-nf-pipeline\n", + "31 Workflow-Corpus-Open-License/canceromics/MeRIPseqPipe\n", + "32 Workflow-Corpus-Open-License/AustralianBioCommons/Nextflow_DSL2_template\n", + "33 Workflow-Corpus-Open-License/AustralianBioCommons/hifi-assembly-workflow\n", + "34 Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/genomic-medicine-sweden/jasen/workflows/bacterial_base.nf': 'quast' is trying to be created as a channel, possibly at line 16. It already exists as a process or a subworkflow in the nextflow file.\n", + "35 Workflow-Corpus-Open-License/stracquadaniolab/cubseq-nf\n", + "36 Workflow-Corpus-Open-License/stracquadaniolab/quick-rnaseq-nf\n", + "37 Workflow-Corpus-Open-License/APHA-CSU/hello-nextflow\n", + "38 Workflow-Corpus-Open-License/eipm/hello-mess-nf\n", + "39 Workflow-Corpus-Open-License/amchakra/tosca\n", + "40 Workflow-Corpus-Open-License/ksumngs/v-met\n", + "41 Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-germline/workflows/cmgg-germline.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 250.\n", + "42 Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/CenterForMedicalGeneticsGhent/nf-cmgg-structural/workflows/cmgg-structural.nf': Not the same number of parameters given as input for the process 'SAMTOOLS_FAIDX', possibly at line 135.\n", + "43 Workflow-Corpus-Open-License/gerlichlab/scshic_pipeline\n", + "44 Workflow-Corpus-Open-License/pblaney/mgp1000\n", + "45 Workflow-Corpus-Open-License/Midnighter/nextflow-utility-services\n", + "46 Workflow-Corpus-Open-License/Midnighter/nf-slack\n", + "47 Workflow-Corpus-Open-License/jnoms/virID\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/jnoms/virID/virID.nf': 'bwa_mem_contigs' is neither a process, subworkflow or an operator. In the executor 'contigs\n", " .join(process_read_pairs.out) | bwa_mem_contigs'.\n", - "48 ../../../Workflow-Corpus-Open-License/BioImageTools/ome-zarr-image-analysis-nextflow\n", - "49 ../../../Workflow-Corpus-Open-License/BioImageTools/baysor-nextflow-module\n", - "50 ../../../Workflow-Corpus-Open-License/NajlaBioinfo/nextflow_tmpl\n", - "51 ../../../Workflow-Corpus-Open-License/didrikolofsson/rmappet\n", - "52 ../../../Workflow-Corpus-Open-License/lemaslab/rump\n", - "53 ../../../Workflow-Corpus-Open-License/replikation/docker_pipelines\n", - "54 ../../../Workflow-Corpus-Open-License/replikation/What_the_Phage\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/replikation/What_the_Phage/phage_deprecated.nf': Something went wrong in an include, possibly at line 135. No such file: '../../../Workflow-Corpus-Open-License/replikation/What_the_Phage/modules/checkV.nf'.\n", - "55 ../../../Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA/main.nf': To much to unpack : The subworkflow 'VALIDATE_FASTQS_WF' emits over one channel in a operation, possibly at line 31.\n", - "56 ../../../Workflow-Corpus-Open-License/wleepang/demo-genomics-workflow-nextflow\n", - "57 ../../../Workflow-Corpus-Open-License/sbilge/nextflow-clinvap\n", - "58 ../../../Workflow-Corpus-Open-License/NickSwainston/nextflow_tutorial\n", - "59 ../../../Workflow-Corpus-Open-License/Hammarn/Nextflow_test\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/Hammarn/Nextflow_test/main.nf': No 'main' workflow was found.\n", - "60 ../../../Workflow-Corpus-Open-License/rdemko2332/downloadFromSra\n", - "61 ../../../Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt/main.nf': No 'main' workflow was found.\n", - "62 ../../../Workflow-Corpus-Open-License/adamd3/BactSeq\n", - "63 ../../../Workflow-Corpus-Open-License/yuukiiwa/CombiPIPE\n", - "64 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/main.nf': Something went wrong in an include, possibly at line 17. No such file: '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/modules/data/test_train_split/test_train_split.nf'.\n", - "65 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern/workflow.nf': No 'main' workflow was found.\n", - "66 ../../../Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search/stacked_ensemble_grid_search.nf': No 'main' workflow was found.\n", - "67 ../../../Workflow-Corpus-Open-License/mgimenez720/plaSquid\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/mgimenez720/plaSquid/workflows/RIPsearch.nf': Not the same number of parameters given as input for the process 'FilterDom', possibly at line 49.\n", - "68 ../../../Workflow-Corpus-Open-License/bahlolab/PLASTER\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/bahlolab/PLASTER/nf/functions.nf': 'path' is expected to be defined in the file, but it could not be found.\n", - "69 ../../../Workflow-Corpus-Open-License/EpiDiverse/snp\n", - "70 ../../../Workflow-Corpus-Open-License/EpiDiverse/ewas\n", - "[9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/ewas/main.nf': A tuple is associated with an call, possibly at line 283. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", - "71 ../../../Workflow-Corpus-Open-License/EpiDiverse/wgbs\n", - "[9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/wgbs/main.nf': A tuple is associated with an call, possibly at line 166. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", - "72 ../../../Workflow-Corpus-Open-License/EpiDiverse/dmr\n", - "[9] Error in the file '../../../Workflow-Corpus-Open-License/EpiDiverse/dmr/main.nf': A tuple is associated with an call, possibly at line 210. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", - "73 ../../../Workflow-Corpus-Open-License/TCLamnidis/contammix_pipeline\n", - "74 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-lofreq\n", - "75 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-bam-preprocessing\n", - "76 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-alignment\n", - "77 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-template\n", - "78 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-vcf-postprocessing\n", - "79 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-hla-hd\n", - "80 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/main.nf': Something went wrong in an include, possibly at line 7. No such file: '../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/nf-core-modules/modules/nf-core/samtools/merge/main.nf'.\n", - "81 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/covigator-ngs-pipeline\n", - "82 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-mutect2\n", - "83 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-strelka2\n", - "84 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-haplotype-caller\n", - "85 ../../../Workflow-Corpus-Open-License/wishabc/nf-aligning\n", - "86 ../../../Workflow-Corpus-Open-License/data-intuitive/diflow\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/data-intuitive/diflow/main.nf': No 'main' workflow was found.\n", - "87 ../../../Workflow-Corpus-Open-License/mribeirodantas/nf-whisper\n", - "88 ../../../Workflow-Corpus-Open-License/ewels/lightweight-template\n", - "89 ../../../Workflow-Corpus-Open-License/darcyabjones/snptree\n", - "90 ../../../Workflow-Corpus-Open-License/darcyabjones/mumflow\n", - "91 ../../../Workflow-Corpus-Open-License/bioinformaticsclouds/nextflow\n", - "92 ../../../Workflow-Corpus-Open-License/sanger-tol/blobtoolkit\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/blobtoolkit/subworkflows/local/minimap_alignment.nf': 'set { ch_aligned }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty()\n", + "48 Workflow-Corpus-Open-License/BioImageTools/ome-zarr-image-analysis-nextflow\n", + "49 Workflow-Corpus-Open-License/BioImageTools/baysor-nextflow-module\n", + "50 Workflow-Corpus-Open-License/NajlaBioinfo/nextflow_tmpl\n", + "51 Workflow-Corpus-Open-License/didrikolofsson/rmappet\n", + "52 Workflow-Corpus-Open-License/lemaslab/rump\n", + "53 Workflow-Corpus-Open-License/replikation/docker_pipelines\n", + "54 Workflow-Corpus-Open-License/replikation/What_the_Phage\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/replikation/What_the_Phage/phage_deprecated.nf': Something went wrong in an include, possibly at line 135. No such file: 'Workflow-Corpus-Open-License/replikation/What_the_Phage/modules/checkV.nf'.\n", + "55 Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/TORCH-Consortium/MAGMA/main.nf': To much to unpack : The subworkflow 'VALIDATE_FASTQS_WF' emits over one channel in a operation, possibly at line 31.\n", + "56 Workflow-Corpus-Open-License/wleepang/demo-genomics-workflow-nextflow\n", + "57 Workflow-Corpus-Open-License/sbilge/nextflow-clinvap\n", + "58 Workflow-Corpus-Open-License/NickSwainston/nextflow_tutorial\n", + "59 Workflow-Corpus-Open-License/Hammarn/Nextflow_test\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/Hammarn/Nextflow_test/main.nf': No 'main' workflow was found.\n", + "60 Workflow-Corpus-Open-License/rdemko2332/downloadFromSra\n", + "61 Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/maxulysse/nextflow_params_opt/main.nf': No 'main' workflow was found.\n", + "62 Workflow-Corpus-Open-License/adamd3/BactSeq\n", + "63 Workflow-Corpus-Open-License/yuukiiwa/CombiPIPE\n", + "64 Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/main.nf': Something went wrong in an include, possibly at line 17. No such file: 'Workflow-Corpus-Open-License/abhi18av/nextflow-datascience-titanic-survival-analysis/modules/data/test_train_split/test_train_split.nf'.\n", + "65 Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow-module-pattern/workflow.nf': No 'main' workflow was found.\n", + "66 Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search/stacked_ensemble_grid_search.nf': No 'main' workflow was found.\n", + "67 Workflow-Corpus-Open-License/mgimenez720/plaSquid\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/mgimenez720/plaSquid/workflows/RIPsearch.nf': Not the same number of parameters given as input for the process 'FilterDom', possibly at line 49.\n", + "68 Workflow-Corpus-Open-License/bahlolab/PLASTER\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/bahlolab/PLASTER/nf/functions.nf': 'path' is expected to be defined in the file, but it could not be found.\n", + "69 Workflow-Corpus-Open-License/EpiDiverse/snp\n", + "70 Workflow-Corpus-Open-License/EpiDiverse/ewas\n", + "[9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/ewas/main.nf': A tuple is associated with an call, possibly at line 283. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", + "71 Workflow-Corpus-Open-License/EpiDiverse/wgbs\n", + "[9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/wgbs/main.nf': A tuple is associated with an call, possibly at line 166. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", + "72 Workflow-Corpus-Open-License/EpiDiverse/dmr\n", + "[9] Error in the file 'Workflow-Corpus-Open-License/EpiDiverse/dmr/main.nf': A tuple is associated with an call, possibly at line 210. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", + "73 Workflow-Corpus-Open-License/TCLamnidis/contammix_pipeline\n", + "74 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-lofreq\n", + "75 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-bam-preprocessing\n", + "76 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-alignment\n", + "77 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-template\n", + "78 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-vcf-postprocessing\n", + "79 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-hla-hd\n", + "80 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/main.nf': Something went wrong in an include, possibly at line 7. No such file: 'Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-copy-number-calling/nf-core-modules/modules/nf-core/samtools/merge/main.nf'.\n", + "81 Workflow-Corpus-Open-License/TRON-Bioinformatics/covigator-ngs-pipeline\n", + "82 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-mutect2\n", + "83 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-strelka2\n", + "84 Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-haplotype-caller\n", + "85 Workflow-Corpus-Open-License/wishabc/nf-aligning\n", + "86 Workflow-Corpus-Open-License/data-intuitive/diflow\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/data-intuitive/diflow/main.nf': No 'main' workflow was found.\n", + "87 Workflow-Corpus-Open-License/mribeirodantas/nf-whisper\n", + "88 Workflow-Corpus-Open-License/ewels/lightweight-template\n", + "89 Workflow-Corpus-Open-License/darcyabjones/snptree\n", + "90 Workflow-Corpus-Open-License/darcyabjones/mumflow\n", + "91 Workflow-Corpus-Open-License/bioinformaticsclouds/nextflow\n", + "92 Workflow-Corpus-Open-License/sanger-tol/blobtoolkit\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/blobtoolkit/subworkflows/local/minimap_alignment.nf': 'set { ch_aligned }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty()\n", " | mix ( MINIMAP2_HIC.out.bam )\n", " | mix ( MINIMAP2_ILMN.out.bam )\n", " | mix ( MINIMAP2_CCS.out.bam )\n", " | mix ( MINIMAP2_CLR.out.bam )\n", " | mix ( MINIMAP2_ONT.out.bam )\n", " | set { ch_aligned }', possibly at line 68.\n", - "93 ../../../Workflow-Corpus-Open-License/sanger-tol/sequencecomposition\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/sequencecomposition/subworkflows/local/fasta_windows.nf': The call for 'TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) )' coudn't be found, before its use in the operation 'ch_compressed_bed = TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) ).output', possibly at line 67. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "94 ../../../Workflow-Corpus-Open-License/sanger-tol/treeval\n", - "95 ../../../Workflow-Corpus-Open-License/sanger-tol/curationpretext\n", - "96 ../../../Workflow-Corpus-Open-License/sanger-tol/gda\n", - "97 ../../../Workflow-Corpus-Open-License/sanger-tol/genomeassembly\n", - "98 ../../../Workflow-Corpus-Open-License/sanger-tol/readmapping\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/readmapping/subworkflows/local/prepare_genome.nf': 'set { ch_bwamem }' is neither a process, subworkflow or an operator. In the executor 'Channel.fromPath ( params.bwamem2_index )\n", + "93 Workflow-Corpus-Open-License/sanger-tol/sequencecomposition\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/sequencecomposition/subworkflows/local/fasta_windows.nf': The call for 'TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) )' coudn't be found, before its use in the operation 'ch_compressed_bed = TABIX_BGZIP ( ch_freq_bed.mix(ch_tsv) ).output', possibly at line 67. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "94 Workflow-Corpus-Open-License/sanger-tol/treeval\n", + "95 Workflow-Corpus-Open-License/sanger-tol/curationpretext\n", + "96 Workflow-Corpus-Open-License/sanger-tol/gda\n", + "97 Workflow-Corpus-Open-License/sanger-tol/genomeassembly\n", + "98 Workflow-Corpus-Open-License/sanger-tol/readmapping\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/readmapping/subworkflows/local/prepare_genome.nf': 'set { ch_bwamem }' is neither a process, subworkflow or an operator. In the executor 'Channel.fromPath ( params.bwamem2_index )\n", " | combine ( ch_fasta )\n", " | map { bwa, meta, fa -> [ meta, bwa ] }\n", " | set { ch_bwamem }', possibly at line 39.\n", - "99 ../../../Workflow-Corpus-Open-License/sanger-tol/genomenote\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/sanger-tol/genomenote/subworkflows/local/genome_statistics.nf': 'set { ch_fastk }' is neither a process, subworkflow or an operator. In the executor 'ch_pacbio.file\n", + "99 Workflow-Corpus-Open-License/sanger-tol/genomenote\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/sanger-tol/genomenote/subworkflows/local/genome_statistics.nf': 'set { ch_fastk }' is neither a process, subworkflow or an operator. In the executor 'ch_pacbio.file\n", " | map { meta, bam -> [ meta + [ id: meta.id.split('_')[0..-2].join('_') ], bam ] }\n", " | groupTuple ( by: [0] )\n", " | set { ch_fastk }', possibly at line 62.\n", - "100 ../../../Workflow-Corpus-Open-License/edgano/TCoffee-NatureProtocol-nf\n", - "101 ../../../Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline/gwas.nf': 'pcrelate' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "102 ../../../Workflow-Corpus-Open-License/montilab/shine-nf\n", - "103 ../../../Workflow-Corpus-Open-License/montilab/pipeliner-2\n", - "104 ../../../Workflow-Corpus-Open-License/mmolari/genome-assembly\n", - "105 ../../../Workflow-Corpus-Open-License/dfornika/cpo-pipeline-nextflow\n", - "106 ../../../Workflow-Corpus-Open-License/dfornika/depth-analysis-nextflow\n", - "107 ../../../Workflow-Corpus-Open-License/rbpisupati/nf-haplocaller\n", - "108 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/lyz-nf\n", - "109 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/demux-nf\n", - "110 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "111 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "112 ../../../Workflow-Corpus-Open-License/tomsing1/nf-tutorial-blast\n", - "113 ../../../Workflow-Corpus-Open-License/idfarbanecha/benchmark-MeSS-CAMISIM\n", - "114 ../../../Workflow-Corpus-Open-License/DHQP/SNVPhyl_Nextflow\n", - "115 ../../../Workflow-Corpus-Open-License/nibscbioinformatics/nf-core-bagobugs\n", - "116 ../../../Workflow-Corpus-Open-License/dchebotarov/nextflow-variant-calling\n", - "117 ../../../Workflow-Corpus-Open-License/HPCBio/16S-rDNA-dada2-pipeline\n", - "118 ../../../Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", - "119 ../../../Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", - "120 ../../../Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", - "121 ../../../Workflow-Corpus-Open-License/SamStudio8/elan-nextflow\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/SamStudio8/elan-nextflow/workflows/elan.nf': Not the same number of parameters given as input for the process 'announce_uploads', possibly at line 14.\n", - "122 ../../../Workflow-Corpus-Open-License/hnawar/nextflow-cloudrun\n", - "123 ../../../Workflow-Corpus-Open-License/robsyme/nf-repeatmasking\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/robsyme/nf-repeatmasking/main.nf': 'recentLTRs' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "124 ../../../Workflow-Corpus-Open-License/robsyme/markerdev\n", - "125 ../../../Workflow-Corpus-Open-License/TARGENE/targene-pipeline\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/TARGENE/targene-pipeline/workflows/targene.nf': The subworkflow 'SVPWorkflow' doesn't emit anything. It is given to an operation, possibly at line 71.\n", - "126 ../../../Workflow-Corpus-Open-License/Boehringer-Ingelheim/flowml-pipeline\n", - "127 ../../../Workflow-Corpus-Open-License/dgarrimar/mvgwas-nf\n", - "128 ../../../Workflow-Corpus-Open-License/dgarrimar/gemma-nf\n", - "129 ../../../Workflow-Corpus-Open-License/axelwalter/diametalyzer\n", - "130 ../../../Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline\n", - "[9] Error in the file '../../../Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline/pipeline.nf': A tuple is associated with an call, possibly at line 288. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", - "131 ../../../Workflow-Corpus-Open-License/oist/LuscombeU_Nextflow_Pipeline_Template\n", - "132 ../../../Workflow-Corpus-Open-License/jhayer/baargin\n", - "133 ../../../Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning\n", - "[9] Error in the file '../../../Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning/gnn_pipeline.nf': A tuple is associated with an call, possibly at line 34. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", - "134 ../../../Workflow-Corpus-Open-License/AndersenLab/ril-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/AndersenLab/ril-nf/main.nf': 'fq_coverage' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "135 ../../../Workflow-Corpus-Open-License/AndersenLab/alignment-nf\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/AndersenLab/alignment-nf/main.nf': '(coverage_id & idxstats_id & flagstat_id & stats_id)' is neither a process, subworkflow or an operator. In the executor 'alignment.out.map { row, bam, bai -> [\"id\", row.id, bam, bai ]} | (coverage_id & idxstats_id & flagstat_id & stats_id)'.\n", - "136 ../../../Workflow-Corpus-Open-License/AndersenLab/nil-ril-nf\n", - "137 ../../../Workflow-Corpus-Open-License/AndersenLab/sv-nf\n", - "138 ../../../Workflow-Corpus-Open-License/AndersenLab/cegwas2-nf\n", - "139 ../../../Workflow-Corpus-Open-License/MaestSi/UMInator\n", - "140 ../../../Workflow-Corpus-Open-License/MaestSi/CharONT2\n", - "141 ../../../Workflow-Corpus-Open-License/MaestSi/nf-m6anet\n", - "142 ../../../Workflow-Corpus-Open-License/MaestSi/pycoMethFlow\n", - "143 ../../../Workflow-Corpus-Open-License/MaestSi/ONTrack2\n", - "144 ../../../Workflow-Corpus-Open-License/phac-nml/mikrokondo\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/phac-nml/mikrokondo/main.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 87.\n", - "145 ../../../Workflow-Corpus-Open-License/lescailab/fenicsmpi\n", - "146 ../../../Workflow-Corpus-Open-License/Pooran-Dewari/SNP_array_nextflow\n", - "147 ../../../Workflow-Corpus-Open-License/Pooran-Dewari/Nextflow-pipeline-Extract-precise-location-of-gimme-maelstrom-TF-motifs\n", - "148 ../../../Workflow-Corpus-Open-License/lars20070/nextflow_lfq\n", - "149 ../../../Workflow-Corpus-Open-License/shaunchuah/cfdna_nextflow\n", - "150 ../../../Workflow-Corpus-Open-License/boulund/metagenome_pipeline\n", - "151 ../../../Workflow-Corpus-Open-License/PGScatalog/pgsc_calc\n", - "152 ../../../Workflow-Corpus-Open-License/ODiogoSilva/innuca-nf\n", - "153 ../../../Workflow-Corpus-Open-License/zamanianlab/Core_smRNAseq-nf\n", - "154 ../../../Workflow-Corpus-Open-License/sysbiomelab/meteor_pipeline\n", - "155 ../../../Workflow-Corpus-Open-License/lstevens17/nemAsm\n", - "156 ../../../Workflow-Corpus-Open-License/grst/minimal-nextflow-template\n", - "157 ../../../Workflow-Corpus-Open-License/grst/nextflow-notebook-pipeline\n", - "158 ../../../Workflow-Corpus-Open-License/grst/bd_rhapsody_velocyto\n", - "159 ../../../Workflow-Corpus-Open-License/grst/universal_analysis_pipeline\n", - "160 ../../../Workflow-Corpus-Open-License/friederhadlich/nextflow_ultraLowInput\n", - "161 ../../../Workflow-Corpus-Open-License/CDCgov/mycosnp-nf\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/CDCgov/mycosnp-nf/subworkflows/local/snpeff_build.nf': 'SNPEFF_BUILD' is expected to be defined in the file, but it could not be found.\n", - "162 ../../../Workflow-Corpus-Open-License/CDCgov/tostadas\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/CDCgov/tostadas/workflows/tostadas.nf': Not the same number of parameters given as input for the process 'UPDATE_SUBMISSION', possibly at line 203.\n", - "163 ../../../Workflow-Corpus-Open-License/MarieLataretu/nextflow-mwe\n", - "164 ../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/workflows/spatial.nf': Something went wrong in an include, possibly at line 46. No such file: '../../../Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/modules/bayestme/nextflow/subworkflows/bayestme/bayestme_basic_visium_analysis/main.nf'.\n", - "165 ../../../Workflow-Corpus-Open-License/SarahMaman/NextflowRNAseq\n", - "166 ../../../Workflow-Corpus-Open-License/angelovangel/nxf-kraken2\n", - "167 ../../../Workflow-Corpus-Open-License/cbcrg/msa-af2-nf\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/cbcrg/msa-af2-nf/main.nf': The call for 'run_seq_aln' coudn't be found, before its use in the operation 'run_seq_aln.out.seq_aln_output.combine(run_psicoffee.out.psicoffee_output, by: 0).combine(dssp_to_fasta.out.dssp_output, by: 0).combine(run_struct_aln.out.struct_output, by: 0).combine(templates, by: 0).combine(structures, by: 0).combine(run_alphafold2.out.af2_models.groupTuple(), by: 0).set{comp_and_eval_input}', possibly at line 73. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "168 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20/rnaseq-flow.nf': No 'main' workflow was found.\n", - "169 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse19\n", - "170 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse21\n", - "171 ../../../Workflow-Corpus-Open-License/cloud303-kloucks/nextflow-debugging\n", - "172 ../../../Workflow-Corpus-Open-License/noamteyssier/pipseq_nextflow\n", - "173 ../../../Workflow-Corpus-Open-License/noamteyssier/10x_rna_velocity_nextflow\n", - "174 ../../../Workflow-Corpus-Open-License/noamteyssier/sciseq_rna_velocity_nextflow\n", - "175 ../../../Workflow-Corpus-Open-License/uct-cbio/bacterial_variant_calling\n", - "176 ../../../Workflow-Corpus-Open-License/ameynert/nf-indelible\n", - "177 ../../../Workflow-Corpus-Open-License/OtimusOne/AFPAP\n", - "178 ../../../Workflow-Corpus-Open-License/nf-wrap/main\n", - "179 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines/subworkflows/hs_pta.nf': The call for 'PICARD_MARKDUPLICATES' coudn't be found, before its use in the operation 'apply_bqsr = PICARD_MARKDUPLICATES.out.dedup_bam.join(GATK_BASERECALIBRATOR.out.table)', possibly at line 175. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "180 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/nextflow-sra-cloud\n", - "181 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/pdx-nextflow\n", - "182 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/crf_nextflow_basics\n", - "183 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/ChIA-PIPE_nextflow\n", - "184 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/mmrSVD\n", - "185 ../../../Workflow-Corpus-Open-License/evanfloden/stable-diffusion-nf\n", - "186 ../../../Workflow-Corpus-Open-License/evanfloden/nf-module-demo\n", - "187 ../../../Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing/main.nf': No 'main' workflow was found.\n", - "188 ../../../Workflow-Corpus-Open-License/HealthInnovationEast/cgpwgs-nf\n", - "189 ../../../Workflow-Corpus-Open-License/HealthInnovationEast/ExpansionHunter\n", - "190 ../../../Workflow-Corpus-Open-License/becavin-lab/nf-blast\n", - "191 ../../../Workflow-Corpus-Open-License/rsuchecki/nextflow-walkthrough\n", - "192 ../../../Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules/bacteria-example.nf': No 'main' workflow was found.\n", - "193 ../../../Workflow-Corpus-Open-License/FischbachLab/nf-reads-profiler\n", - "194 ../../../Workflow-Corpus-Open-License/FischbachLab/nf-blast\n", - "195 ../../../Workflow-Corpus-Open-License/utia-gc/ngs\n", - "196 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-template\n", - "197 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-wf-megSAP\n", - "198 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-rnaseq\n", - "199 ../../../Workflow-Corpus-Open-License/JacobLay/NextflowIntro\n", - "200 ../../../Workflow-Corpus-Open-License/OpenMSConsulting/NextflowLFQ\n", - "201 ../../../Workflow-Corpus-Open-License/vibbits/chipseq-nextflow\n", - "202 ../../../Workflow-Corpus-Open-License/OlgaChern/nextflow_gentrius_sim\n", - "203 ../../../Workflow-Corpus-Open-License/bkohrn/picard_demux_nextflow\n", - "204 ../../../Workflow-Corpus-Open-License/manuelesimi/hello-nextflow\n", - "205 ../../../Workflow-Corpus-Open-License/kkerns85/midas_nf_tower\n", - "206 ../../../Workflow-Corpus-Open-License/microgenlab/porefile\n", - "207 ../../../Workflow-Corpus-Open-License/open2c/distiller-nf\n", - "208 ../../../Workflow-Corpus-Open-License/MiGurke/nfmap\n", - "209 ../../../Workflow-Corpus-Open-License/MiGurke/nfvacal\n", - "210 ../../../Workflow-Corpus-Open-License/MiGurke/nfcongeneus\n", - "211 ../../../Workflow-Corpus-Open-License/tluquez/QUARS\n", - "212 ../../../Workflow-Corpus-Open-License/zhanyinx/metagenomics\n", - "213 ../../../Workflow-Corpus-Open-License/aertslab/SpatialNF\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/aertslab/SpatialNF/main.nf': No 'main' workflow was found.\n", - "214 ../../../Workflow-Corpus-Open-License/aertslab/scenic-nf\n", - "215 ../../../Workflow-Corpus-Open-License/systems-genomics-lab/next-bgc\n", - "216 ../../../Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert/modules/processes.nf': Multiple 'input:' were found in the process 'Convert_EachFileFromRoot2SeparateOMETIFF'.\n", - "217 ../../../Workflow-Corpus-Open-License/bioShaun/om-nf-prepare\n", - "218 ../../../Workflow-Corpus-Open-License/bioShaun/xms-rnaseq-nf\n", - "219 ../../../Workflow-Corpus-Open-License/lepsalex/results\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/lepsalex/results/debug/calls.nf': No 'main' workflow was found.\n", - "220 ../../../Workflow-Corpus-Open-License/lepsalex/nextflow-pcawg-bwa-mem-workflow\n", - "221 ../../../Workflow-Corpus-Open-License/HadrienG/nanoflow\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/HadrienG/nanoflow/main.nf': 'assembly' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "222 ../../../Workflow-Corpus-Open-License/HadrienG/nextflow_rna\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/HadrienG/nextflow_rna/rna.nf': No 'main' workflow was found.\n", - "223 ../../../Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support/functions.nf': No 'main' workflow was found.\n", - "224 ../../../Workflow-Corpus-Open-License/hoelzer/nf-hmmsearch\n", - "225 ../../../Workflow-Corpus-Open-License/hoelzer/dammit-nf\n", - "226 ../../../Workflow-Corpus-Open-License/hoelzer/virify\n", - "227 ../../../Workflow-Corpus-Open-License/peterk87/nf-flu\n", - "228 ../../../Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline/virify.nf': Not the same number of parameters given as input for the subworklfow 'annotate' in the call, possibly at line 649.\n", - "229 ../../../Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc/modules/local/custom.nf': Multiple 'output:' were found in the process 'processGVCF'?\n", - "230 ../../../Workflow-Corpus-Open-License/jagedn/nextflow-groogle-sheet\n", - "231 ../../../Workflow-Corpus-Open-License/B-UMMI/DEN-IM\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/B-UMMI/DEN-IM/DEN-IM.nf': 'compile_status_buffer' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "232 ../../../Workflow-Corpus-Open-License/openproblems-bio/openproblems-v2\n", - "233 ../../../Workflow-Corpus-Open-License/PRIDE-Archive/pride-molecule-indexer\n", - "234 ../../../Workflow-Corpus-Open-License/DaneVass/BARtab\n", - "235 ../../../Workflow-Corpus-Open-License/LeoniePohl/nextflow-diffexp-testpipeline\n", - "236 ../../../Workflow-Corpus-Open-License/stenglein-lab/viral_variant_caller\n", - "237 ../../../Workflow-Corpus-Open-License/jemunro/Tidy-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/jemunro/Tidy-nf/example.nf': No 'main' workflow was found.\n", - "238 ../../../Workflow-Corpus-Open-License/mattfemia/scrnaseq-pipeline\n", - "239 ../../../Workflow-Corpus-Open-License/MHH-RCUG/nf_wochenende\n", - "240 ../../../Workflow-Corpus-Open-License/DarianHole/test-nextflow\n", - "241 ../../../Workflow-Corpus-Open-License/fmalmeida/MpGAP\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/fmalmeida/MpGAP/workflows/hybrid.nf': Multiple 'main:' were found in the subworkflow 'HYBRID'.\n", - "242 ../../../Workflow-Corpus-Open-License/fmalmeida/bacannot\n", - "243 ../../../Workflow-Corpus-Open-License/uel3/UnO_nf\n", - "244 ../../../Workflow-Corpus-Open-License/nttg8100/Simple-RNA-seq-Nextflow-with-Salmon\n", - "245 ../../../Workflow-Corpus-Open-License/fredjaya/msmc-nf\n", - "246 ../../../Workflow-Corpus-Open-License/pgonzale60/nxf_pipelines\n", - "247 ../../../Workflow-Corpus-Open-License/noepozzan/small-peptide-pipeline\n", - "248 ../../../Workflow-Corpus-Open-License/lukfor/pgs-calc-nf\n", - "249 ../../../Workflow-Corpus-Open-License/biocorecrg/contamination-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/biocorecrg/contamination-nf/main.nf': Not the same number of opening and closing curlies '{}' in the file.\n", - "250 ../../../Workflow-Corpus-Open-License/biocorecrg/nf-cloud-gpu-test\n", - "251 ../../../Workflow-Corpus-Open-License/biocorecrg/MOP2\n", - "252 ../../../Workflow-Corpus-Open-License/biocorecrg/nextflow_detached_db_wrapper\n", - "253 ../../../Workflow-Corpus-Open-License/NCBI-Hackathons/ATACFlow\n", - "254 ../../../Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW/align.nf': Not the same number of opening and closing curlies '{}' in the file.\n", - "255 ../../../Workflow-Corpus-Open-License/breichholf/smRNAseq\n", - "256 ../../../Workflow-Corpus-Open-License/nextflow-io/cwl2nxf\n", - "257 ../../../Workflow-Corpus-Open-License/nextflow-io/nf-ffq\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/nextflow-io/nf-ffq/ffq.nf': No 'main' workflow was found.\n", - "258 ../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/main.nf': Something went wrong in an include, possibly at line 76. No such file: '../../../Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/${subwork_folder}/fastqc.nf'.\n", - "259 ../../../Workflow-Corpus-Open-License/nextflow-io/gccbosc18-training\n", - "260 ../../../Workflow-Corpus-Open-License/nextflow-io/socks\n", - "261 ../../../Workflow-Corpus-Open-License/JackCurragh/Nextflow-Template\n", - "262 ../../../Workflow-Corpus-Open-License/ZuberLab/mageck-nf\n", - "263 ../../../Workflow-Corpus-Open-License/ZuberLab/vbcf-nf\n", - "264 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-mageck-nf\n", - "265 ../../../Workflow-Corpus-Open-License/ZuberLab/guidemapper-nf\n", - "266 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-process-nf\n", - "267 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-nf\n", - "268 ../../../Workflow-Corpus-Open-License/ZuberLab/sra-nf\n", - "269 ../../../Workflow-Corpus-Open-License/oxfordfun/FunSnippy\n", - "270 ../../../Workflow-Corpus-Open-License/mmatthews06/nextflow-playground\n", - "271 ../../../Workflow-Corpus-Open-License/ricomnl/bioinformatics-pipeline-tutorial\n", - "272 ../../../Workflow-Corpus-Open-License/dolphinnext/rnaseq\n", - "273 ../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'.\n", - "274 ../../../Workflow-Corpus-Open-License/hoelzer-lab/rnaflow\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/hoelzer-lab/rnaflow/main.nf': 'sortmerna' is trying to be created as a channel, possibly at line 475. It already exists as a process or a subworkflow in the nextflow file.\n", - "275 ../../../Workflow-Corpus-Open-License/isugifNF/blast\n", - "276 ../../../Workflow-Corpus-Open-License/vmikk/BatchBlaster\n", - "277 ../../../Workflow-Corpus-Open-License/vmikk/PhyloNext\n", - "278 ../../../Workflow-Corpus-Open-License/bschiffthaler/nf-modules\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/bschiffthaler/nf-modules/multiqc.nf': No 'main' workflow was found.\n", - "279 ../../../Workflow-Corpus-Open-License/pcrxn/ProkkaFlow\n", - "280 ../../../Workflow-Corpus-Open-License/alneberg/trigger_error_nf\n", - "281 ../../../Workflow-Corpus-Open-License/opencobra/jeweler\n", - "282 ../../../Workflow-Corpus-Open-License/faithman/variant-nf\n", - "283 ../../../Workflow-Corpus-Open-License/digenoma-lab/nf-groot\n", - "284 ../../../Workflow-Corpus-Open-License/digenoma-lab/k-count-nf\n", - "285 ../../../Workflow-Corpus-Open-License/ATpoint/nf_findMotifs\n", - "286 ../../../Workflow-Corpus-Open-License/eQTL-Catalogue/colocalisation\n", - "287 ../../../Workflow-Corpus-Open-License/eQTL-Catalogue/susie-workflow\n", - "288 ../../../Workflow-Corpus-Open-License/veidenberg/tools-api-nextflow\n", - "289 ../../../Workflow-Corpus-Open-License/RibosomeCRCL/ribomethseq-nf\n", - "290 ../../../Workflow-Corpus-Open-License/anajung/CZI_addon\n", - "291 ../../../Workflow-Corpus-Open-License/cometsong/gbrs_nxf\n", - "292 ../../../Workflow-Corpus-Open-License/cometsong/ATAC_Seq_nxf\n", - "293 ../../../Workflow-Corpus-Open-License/jvierstra/nf-rnaseq\n", - "294 ../../../Workflow-Corpus-Open-License/RHReynolds/mkfastq\n", - "295 ../../../Workflow-Corpus-Open-License/bactopia/bactopia\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/bactopia/bactopia/workflows/teton.nf': Something went wrong in an include, possibly at line 33. No such file: '../../../Workflow-Corpus-Open-License/bactopia/bactopia/modules/local/bactopia/gather_samples/main.nf'.\n", - "296 ../../../Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis/modules/nf-core/modules/blast/makeblastdb/main.nf': 'SIGS_BLAST_MAKEBLASTDB' is expected to be defined in the file, but it could not be found.\n", - "297 ../../../Workflow-Corpus-Open-License/tiagofilipe12/pATLASflow\n", - "298 ../../../Workflow-Corpus-Open-License/usafsam/mad_river_wf\n", - "299 ../../../Workflow-Corpus-Open-License/sebgoti/spatial-pipeline\n", - "300 ../../../Workflow-Corpus-Open-License/esteinig/nf-mvp\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/esteinig/nf-mvp/lib/utils.nf': 'getSubsampleReads' is expected to be defined in the file, but it could not be found.\n", - "301 ../../../Workflow-Corpus-Open-License/cedarwarman/pollen_cv_nextflow\n", - "302 ../../../Workflow-Corpus-Open-License/lehtiolab/nf-msconvert\n", - "303 ../../../Workflow-Corpus-Open-License/lehtiolab/ddamsproteomics\n", - "304 ../../../Workflow-Corpus-Open-License/stajichlab/nf-comparative-genomics\n", - "305 ../../../Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines/main.nf': No 'main' workflow was found.\n", - "306 ../../../Workflow-Corpus-Open-License/oalmelid/lift-over-nf\n", - "307 ../../../Workflow-Corpus-Open-License/dmalzl/howto-nf\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/dmalzl/howto-nf/workflows/chipseq.nf': 'CHIPSEQ' is expected to be defined in the file, but it could not be found.\n", - "308 ../../../Workflow-Corpus-Open-License/eastgenomics/mutect2_nextflow\n", - "309 ../../../Workflow-Corpus-Open-License/eastgenomics/VerifyBamID_nextflow\n", - "310 ../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_assembly-nf\n", - "311 ../../../Workflow-Corpus-Open-License/BU-ISCIII/panelLowFreq-nf\n", - "312 ../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training/main.nf': 'srst2_resistance' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "313 ../../../Workflow-Corpus-Open-License/AllenInstitute/deepinterpolation_nextflow\n", - "314 ../../../Workflow-Corpus-Open-License/sergpolly/random-nextflow-utils\n", - "315 ../../../Workflow-Corpus-Open-License/CIBERER-pipelines/mosaicism_nextflow\n", - "316 ../../../Workflow-Corpus-Open-License/EnriqueDoster/bioinformatic-nextflow-pipelines\n", - "317 ../../../Workflow-Corpus-Open-License/AlfredUg/QuasiFlow\n", - "318 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-model2data\n", - "319 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synstage\n", - "320 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synindex\n", - "321 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-genie\n", - "322 ../../../Workflow-Corpus-Open-License/vntasis/stan-nf\n", - "323 ../../../Workflow-Corpus-Open-License/maxibor/kraken-nf\n", - "324 ../../../Workflow-Corpus-Open-License/maxibor/organdiet\n", - "325 ../../../Workflow-Corpus-Open-License/nkrumm/hello\n", - "326 ../../../Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice/somatic_vardict_pindel.nf': Multiple 'when:' were found in the process 'cnv_oncocnv_tumor_controls'.\n", - "327 ../../../Workflow-Corpus-Open-License/GunzIvan28/nextflow-rMAP-devt\n", - "328 ../../../Workflow-Corpus-Open-License/CCBR/CHAMPAGNE\n", - "329 ../../../Workflow-Corpus-Open-License/CCBR/CCBR_NextflowTemplate\n", - "330 ../../../Workflow-Corpus-Open-License/gleisonm/nextflow_bigscape\n", - "331 ../../../Workflow-Corpus-Open-License/aws-samples/aws-gatk-recipe-nextflow-pipeline\n", - "332 ../../../Workflow-Corpus-Open-License/thanhleviet/nextflow-ratt\n", - "333 ../../../Workflow-Corpus-Open-License/transXpress/transXpress-nextflow\n", - "334 ../../../Workflow-Corpus-Open-License/marc-jones/nextflow-example\n", - "335 ../../../Workflow-Corpus-Open-License/kenibrewer/shapeseq\n", - "336 ../../../Workflow-Corpus-Open-License/kenibrewer/simplenextflow\n", - "337 ../../../Workflow-Corpus-Open-License/gwright99/hello-nonmain\n", - "338 ../../../Workflow-Corpus-Open-License/jtmccr1/beast_analysis\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/jtmccr1/beast_analysis/beast_analysis.nf': Multiple 'input:' were found in the process 'mcc'.\n", - "339 ../../../Workflow-Corpus-Open-License/crashGoBoom/nf-video\n", - "340 ../../../Workflow-Corpus-Open-License/Dowell-Lab/RNAseq-Flow\n", - "341 ../../../Workflow-Corpus-Open-License/Dowell-Lab/Bidirectional-Flow\n", - "342 ../../../Workflow-Corpus-Open-License/Dowell-Lab/Analysis-Flow\n", - "343 ../../../Workflow-Corpus-Open-License/Dowell-Lab/ChIP-Flow\n", - "344 ../../../Workflow-Corpus-Open-License/bguo068/snp_call_nf\n", - "345 ../../../Workflow-Corpus-Open-License/bguo068/posseleff_empirical\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/bguo068/posseleff_empirical/01_filter_vcf.nf': Not the same number of parameters given as input for the process 'BCFTOOLS_VIEW_FILTER_SAMPLE_BY_IMISS1', possibly at line 165.\n", - "346 ../../../Workflow-Corpus-Open-License/salzman-lab/SpliZ\n", - "347 ../../../Workflow-Corpus-Open-License/KohlbacherLab/nextflow-clinvap\n", - "348 ../../../Workflow-Corpus-Open-License/ChrisgKent/flye-on-cluster\n", - "349 ../../../Workflow-Corpus-Open-License/RenneLab/CnR-flow\n", - "350 ../../../Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia/subworkflows/encyclopedia.nf': 'set { global_files }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() | set { global_files }', possibly at line 89.\n", - "351 ../../../Workflow-Corpus-Open-License/shenwei356/blast-nf\n", - "352 ../../../Workflow-Corpus-Open-License/ralsallaq/metaGx_nf\n", - "353 ../../../Workflow-Corpus-Open-License/ikmb-denbi/genome-annotation\n", - "354 ../../../Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines/main.nf': Not the same number of opening and closing parentheses '()' in the file.\n", - "355 ../../../Workflow-Corpus-Open-License/sauriiiin/rnaseeker\n", - "356 ../../../Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline/main.nf': 'hardfilters_snp' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "357 ../../../Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow/subworkflows/abinitio_training/main.nf': Not the same number of parameters given as input for the process 'BLAST_BLASTP', possibly at line 54.\n", - "358 ../../../Workflow-Corpus-Open-License/FloWuenne/nextflow_saige_dsl2\n", - "359 ../../../Workflow-Corpus-Open-License/FloWuenne/meta-METAL_nextflow_dsl2\n", - "360 ../../../Workflow-Corpus-Open-License/olgabot/nextflow-test-aws\n", - "361 ../../../Workflow-Corpus-Open-License/heuermh/minnebar15-workflow\n", - "362 ../../../Workflow-Corpus-Open-License/kviljoen/uct-srst2\n", - "363 ../../../Workflow-Corpus-Open-License/kviljoen/EMIRGE_nextflow\n", - "364 ../../../Workflow-Corpus-Open-License/tuzov/nf-cg-helloworld\n", - "365 ../../../Workflow-Corpus-Open-License/t-neumann/salmon-nf\n", - "366 ../../../Workflow-Corpus-Open-License/FredHutch/souper-star\n", - "367 ../../../Workflow-Corpus-Open-License/FredHutch/VMAA\n", - "368 ../../../Workflow-Corpus-Open-License/FredHutch/workflow-template-nextflow\n", - "369 ../../../Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline/rnaseq_script.nf': No 'main' workflow was found.\n", - "370 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_4\n", - "371 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1_print_hello_world\n", - "372 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1\n", - "373 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_5\n", - "374 ../../../Workflow-Corpus-Open-License/danielecook/nextflow-tutorial\n", - "375 ../../../Workflow-Corpus-Open-License/rnajena/RNAswarm\n", - "376 ../../../Workflow-Corpus-Open-License/tdelhomme/vcf_ancestry-nf\n", - "377 ../../../Workflow-Corpus-Open-License/tdelhomme/SimulateLowCovSeq-nf\n", - "378 ../../../Workflow-Corpus-Open-License/tdelhomme/variantfiltering-nf\n", - "379 ../../../Workflow-Corpus-Open-License/tdelhomme/RegionalEnrichment-nf\n", - "380 ../../../Workflow-Corpus-Open-License/tdelhomme/SV-simulation-nf\n", - "381 ../../../Workflow-Corpus-Open-License/PavriLab/repliseq-nf\n", - "382 ../../../Workflow-Corpus-Open-License/PavriLab/geneIS-nf\n", - "383 ../../../Workflow-Corpus-Open-License/PavriLab/hicer-nf\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/PavriLab/hicer-nf/workflows/hicer.nf': To much to unpack : The subworkflow 'PREPARE_GENOME' emits over one channel in a operation, possibly at line 146.\n", - "384 ../../../Workflow-Corpus-Open-License/gp201/Freyja_pathogen_workflow_alpha\n", - "385 ../../../Workflow-Corpus-Open-License/IARCbioinfo/LiftOver-nf\n", - "386 ../../../Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file.\n", - "387 ../../../Workflow-Corpus-Open-License/IARCbioinfo/TCGA_platypus-nf\n", - "388 ../../../Workflow-Corpus-Open-License/IARCbioinfo/CODEX-nf\n", - "389 ../../../Workflow-Corpus-Open-License/IARCbioinfo/purple-nf\n", - "390 ../../../Workflow-Corpus-Open-License/IARCbioinfo/table_annovar-nf\n", - "391 ../../../Workflow-Corpus-Open-License/IARCbioinfo/octopus-nf\n", - "392 ../../../Workflow-Corpus-Open-License/IARCbioinfo/damage-estimator-nf\n", - "393 ../../../Workflow-Corpus-Open-License/IARCbioinfo/NGSCheckMate-nf\n", - "394 ../../../Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf/main.nf': 'arriba' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "395 ../../../Workflow-Corpus-Open-License/IARCbioinfo/gatk4-DataPreProcessing-nf\n", - "396 ../../../Workflow-Corpus-Open-License/IARCbioinfo/template-nf\n", - "397 ../../../Workflow-Corpus-Open-License/IARCbioinfo/ampliconarchitect-nf\n", - "398 ../../../Workflow-Corpus-Open-License/IARCbioinfo/bamsurgeon-nf\n", - "399 ../../../Workflow-Corpus-Open-License/IARCbioinfo/BQSR-nf\n", - "400 ../../../Workflow-Corpus-Open-License/jianhong/universalModule\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/jianhong/universalModule/chipseq.nf': Something went wrong in an include, possibly at line 14. No such file: '../../../Workflow-Corpus-Open-License/jianhong/universalModule/loadModule(checksum,.nf'.\n", - "401 ../../../Workflow-Corpus-Open-License/jianhong/nextflowTutorial\n", - "402 ../../../Workflow-Corpus-Open-License/likelet/ExomePipe\n", - "403 ../../../Workflow-Corpus-Open-License/bentsherman/tesseract\n", - "404 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/dragonflye-nf\n", - "405 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/covflo\n", - "406 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/fluflo\n", - "407 ../../../Workflow-Corpus-Open-License/bhargava-morampalli/cdnaseqont-nextflow\n", - "408 ../../../Workflow-Corpus-Open-License/pandora414/ssnp\n", - "409 ../../../Workflow-Corpus-Open-License/pandora414/lncRNA\n", - "410 ../../../Workflow-Corpus-Open-License/austinreidmanny/tvv-nf\n", - "411 ../../../Workflow-Corpus-Open-License/stevekm/nextflow-communicator\n", - "412 ../../../Workflow-Corpus-Open-License/stevekm/newfile-detector-nf\n", - "413 ../../../Workflow-Corpus-Open-License/keoughkath/GBGCnf\n", - "414 ../../../Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline/subworkflow/SNV.nf': 'SNV' is trying to be created as a channel, possibly at line 27. It already exists as a process or a subworkflow in the nextflow file.\n", - "415 ../../../Workflow-Corpus-Open-License/team113sanger/t113_irods_to_lustre\n", - "416 ../../../Workflow-Corpus-Open-License/BrianLohman/pdx-nf\n", - "417 ../../../Workflow-Corpus-Open-License/BrianLohman/ctseq-nf\n", - "418 ../../../Workflow-Corpus-Open-License/BrianLohman/RNAseq-variant-calling-nf\n", - "419 ../../../Workflow-Corpus-Open-License/BrianLohman/cellranger-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/BrianLohman/cellranger-nf/main.nf': An odd number of '\"\"\"' was found in the code.\n", - "420 ../../../Workflow-Corpus-Open-License/WarrenLab/longread-polish-nf\n", - "421 ../../../Workflow-Corpus-Open-License/WarrenLab/longread-svs-nf\n", - "422 ../../../Workflow-Corpus-Open-License/WarrenLab/shortread-polish-nf\n", - "423 ../../../Workflow-Corpus-Open-License/WarrenLab/purge-haplotigs-nf\n", - "424 ../../../Workflow-Corpus-Open-License/WarrenLab/minigraph-cactus-nf\n", - "425 ../../../Workflow-Corpus-Open-License/WarrenLab/cellranger-nf\n", - "426 ../../../Workflow-Corpus-Open-License/WarrenLab/hic-scaffolding-nf\n", - "427 ../../../Workflow-Corpus-Open-License/limrp/nextflow_metagenomics\n", - "428 ../../../Workflow-Corpus-Open-License/limrp/nextflow_subworkflow\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/limrp/nextflow_subworkflow/subworkflows/local/fasta_metaprodigal_cdhit.nf': Not the same number of parameters given as input for the process 'PRODIGAL', possibly at line 21.\n", - "429 ../../../Workflow-Corpus-Open-License/zajakin/sRNAflow\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/zajakin/sRNAflow/sRNAflow.nf': No 'main' workflow was found.\n", - "430 ../../../Workflow-Corpus-Open-License/seqeralabs/nf-canary\n", - "431 ../../../Workflow-Corpus-Open-License/arontommi/RNAseq-VAX\n", - "432 ../../../Workflow-Corpus-Open-License/ObenaufLab/snv-calling-nf\n", - "433 ../../../Workflow-Corpus-Open-License/ObenaufLab/sv-calling-nf\n", - "434 ../../../Workflow-Corpus-Open-License/ObenaufLab/virus-detection-nf\n", - "435 ../../../Workflow-Corpus-Open-License/Streit-lab/enhancer_annotation_and_motif_analysis\n", - "436 ../../../Workflow-Corpus-Open-License/kullrich/snpless-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/kullrich/snpless-nf/main.nf': 'genmap' is trying to be created as a channel, possibly at line 263. It already exists as a process or a subworkflow in the nextflow file.\n", - "437 ../../../Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel/flaq_amr_plus2.nf': Not the same number of parameters given as input for the process 'plusAnalyses'.\n", - "438 ../../../Workflow-Corpus-Open-License/PAIN-initiative/nextflow-scRNAseq\n", - "439 ../../../Workflow-Corpus-Open-License/Ratoncito/callingcards\n", - "440 ../../../Workflow-Corpus-Open-License/x-kiana/nextflow_pipeline\n", - "441 ../../../Workflow-Corpus-Open-License/cellgeni/nf-workshop\n", - "442 ../../../Workflow-Corpus-Open-License/cellgeni/rnaseq\n", - "443 ../../../Workflow-Corpus-Open-License/cellgeni/scmapIndex\n", - "444 ../../../Workflow-Corpus-Open-License/evotools/nSPECTRa\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/evotools/nSPECTRa/include/workflow/mutyper.nf': 'chromosomeList' is trying to be created as a channel, possibly at line 10. It already exists as a process or a subworkflow in the nextflow file.\n", - "445 ../../../Workflow-Corpus-Open-License/evotools/nf-LO\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/evotools/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found.\n", - "446 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/fastqc-nf\n", - "447 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/bamQC-nf\n", - "448 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/Germline-StructuralV-nf\n", - "449 ../../../Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf/main.nf': No 'main' workflow was found.\n", - "450 ../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/main.nf': Something went wrong in an include, possibly at line 68. No such file: '../../../Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/${subwork_folder}/tools.nf'.\n", - "451 ../../../Workflow-Corpus-Open-License/mlf-core/nextflow-lcep\n", - "452 ../../../Workflow-Corpus-Open-License/wbazant/nextflow-hello-dsl2\n", - "453 ../../../Workflow-Corpus-Open-License/palfalvi/rnaseq\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/palfalvi/rnaseq/main.nf': The call for 'run_fastSE_qc' coudn't be found, before its use in the operation 'salmon_quantSE.out.collect().concat(run_fastSE_qc.out.collect())', possibly at line 217. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "454 ../../../Workflow-Corpus-Open-License/samlhao/nf-core-abricate\n", - "455 ../../../Workflow-Corpus-Open-License/samlhao/hgtsimulation\n", - "456 ../../../Workflow-Corpus-Open-License/samlhao/nextflow-spid\n", - "457 ../../../Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics/main.nf': No 'main' workflow was found.\n", - "458 ../../../Workflow-Corpus-Open-License/robomics/generate_higlass_gene_track\n", - "459 ../../../Workflow-Corpus-Open-License/alexthiery/modify-gtf\n", - "460 ../../../Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow/main.nf': 'PCA' is trying to be created as a channel, possibly at line 1. It already exists as a process or a subworkflow in the nextflow file.\n", - "461 ../../../Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf/main.nf': Not the same number of parameters given as input for the process 'freebayes', possibly at line 159.\n", - "462 ../../../Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline/modules/messages.nf': 'startMessage' is expected to be defined in the file, but it could not be found.\n", - "463 ../../../Workflow-Corpus-Open-License/mpieva/quicksand\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/mpieva/quicksand/workflows/00_setup.nf': 'setup' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file.\n", - "464 ../../../Workflow-Corpus-Open-License/Mxrcon/Savio_alignments_nf\n", - "465 ../../../Workflow-Corpus-Open-License/csiro-crop-informatics/repset\n", - "466 ../../../Workflow-Corpus-Open-License/csiro-crop-informatics/nextflow-embl-abr-webinar\n", - "467 ../../../Workflow-Corpus-Open-License/mhebrard/TrimFlow\n", - "468 ../../../Workflow-Corpus-Open-License/jowkar/xenocell_nextflow\n", - "469 ../../../Workflow-Corpus-Open-License/tthyer/nextflow-scratch\n", - "470 ../../../Workflow-Corpus-Open-License/julesjacobsen/nextflow-test\n", - "471 ../../../Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell/main.nf': Not the same number of parameters given as input for the process 'ENA_DOWNLOAD', possibly at line 123.\n", - "472 ../../../Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline/main.nf': No 'main' workflow was found.\n", - "473 ../../../Workflow-Corpus-Open-License/bts76-pitt/BCR_nextflow\n", - "474 ../../../Workflow-Corpus-Open-License/dnieuw/ENA_SARS_Cov2_nanopore\n", - "475 ../../../Workflow-Corpus-Open-License/nf-modules-hub/mykrobe\n", - "476 ../../../Workflow-Corpus-Open-License/nf-modules-hub/tb-profiler\n", - "477 ../../../Workflow-Corpus-Open-License/nf-modules-hub/mtbseq\n", - "478 ../../../Workflow-Corpus-Open-License/nf-modules-hub/gzip\n", - "479 ../../../Workflow-Corpus-Open-License/nf-modules-hub/snippy\n", - "480 ../../../Workflow-Corpus-Open-License/nf-modules-hub/trimmomatic\n", - "481 ../../../Workflow-Corpus-Open-License/nf-modules-hub/rd-analyzer\n", - "482 ../../../Workflow-Corpus-Open-License/nf-modules-hub/prokka\n", - "483 ../../../Workflow-Corpus-Open-License/nf-modules-hub/spotyping\n", - "484 ../../../Workflow-Corpus-Open-License/nf-modules-hub/kvarq\n", - "485 ../../../Workflow-Corpus-Open-License/nf-modules-hub/multiqc\n", - "486 ../../../Workflow-Corpus-Open-License/nf-modules-hub/nextflow_hub_process\n", - "487 ../../../Workflow-Corpus-Open-License/nf-modules-hub/quast\n", - "488 ../../../Workflow-Corpus-Open-License/nf-modules-hub/spades\n", - "489 ../../../Workflow-Corpus-Open-License/nf-modules-hub/rclone\n", - "490 ../../../Workflow-Corpus-Open-License/nf-modules-hub/fastqc\n", - "491 ../../../Workflow-Corpus-Open-License/mja/ukb-release-nf\n", - "492 ../../../Workflow-Corpus-Open-License/asereewit/rsv_ampseq\n", - "493 ../../../Workflow-Corpus-Open-License/scilus/dmriqc_flow\n", - "494 ../../../Workflow-Corpus-Open-License/RenzoTale88/nf-LO\n", - "[18] Error in the file '../../../Workflow-Corpus-Open-License/RenzoTale88/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found.\n", - "495 ../../../Workflow-Corpus-Open-License/khigashi1987/CUTRUN_Nextflow\n", - "496 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek/subworkflows/local/preprocessing_read_qc.nf': Multiple 'emit:' were found in the subworkflow 'PREPROCESSING_READ_QC'. \n", - "497 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Nextstrain_Build\n", - "498 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret/subworkflows/msa.nf': 'msa' is trying to be created as a channel, possibly at line 7. It already exists as a process or a subworkflow in the nextflow file.\n", - "499 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls/workflows/assembly.nf': 'assembly' is trying to be created as a channel, possibly at line 11. It already exists as a process or a subworkflow in the nextflow file.\n", - "500 ../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur/subworkflows/average_nucleotide_identity.nf': 'datasets_summary' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file.\n", - "501 ../../../Workflow-Corpus-Open-License/jallen73/teloSealer\n", - "502 ../../../Workflow-Corpus-Open-License/sidorov-si/nextflow-example-start\n", - "503 ../../../Workflow-Corpus-Open-License/gongyh/nf-core-scp\n", - "504 ../../../Workflow-Corpus-Open-License/gongyh/nf-core-scgs\n", - "505 ../../../Workflow-Corpus-Open-License/ikmb/nf-template\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/ikmb/nf-template/main.nf': Not the same number of parameters given as input for the subworklfow 'MAIN' in the call, possibly at line 38.\n", - "506 ../../../Workflow-Corpus-Open-License/ikmb/gwas-qc\n", - "507 ../../../Workflow-Corpus-Open-License/ikmb/gwas-assoc\n", - "508 ../../../Workflow-Corpus-Open-License/ikmb/finemapping\n", - "509 ../../../Workflow-Corpus-Open-License/ikmb/TOFU-MAaPO\n", - "510 ../../../Workflow-Corpus-Open-License/h3abionet/TADA\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/h3abionet/TADA/main.nf': Multiple 'when:' were found in the process 'ToQIIME2Aln'.\n", - "511 ../../../Workflow-Corpus-Open-License/phue/GWAS-nf\n", - "512 ../../../Workflow-Corpus-Open-License/athbaltzis/paralogs-nf\n", - "513 ../../../Workflow-Corpus-Open-License/athbaltzis/diff-AS-nf\n", - "514 ../../../Workflow-Corpus-Open-License/apeltzer/IGCG-featureCounts\n", - "515 ../../../Workflow-Corpus-Open-License/Biocentric/DeepVariantNF\n", - "516 ../../../Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns/emit_example.nf': The call for 'doo_foo' coudn't be found, before its use in the operation 'doo_foo.out.foo_item', possibly at line 44. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "517 ../../../Workflow-Corpus-Open-License/vierstralab/nf-genotyping\n", - "518 ../../../Workflow-Corpus-Open-License/vierstralab/nf-index\n", - "519 ../../../Workflow-Corpus-Open-License/guigolab/FA-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/FA-nf/main.nf': Not the same number of opening and closing parentheses '()' in the file.\n", - "520 ../../../Workflow-Corpus-Open-License/guigolab/selenoprofiles-nf\n", - "521 ../../../Workflow-Corpus-Open-License/guigolab/sqtlseeker2-nf\n", - "522 ../../../Workflow-Corpus-Open-License/guigolab/geneidx\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/geneidx/main.nf': Something went wrong in an include, possibly at line 34. No such file: '../../../Workflow-Corpus-Open-License/guigolab/geneidx/${wk_folder}/GENEIDX.nf'.\n", - "523 ../../../Workflow-Corpus-Open-License/guigolab/ipsa-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/guigolab/ipsa-nf/ipsa.nf': 'ssjA06' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "524 ../../../Workflow-Corpus-Open-License/quinlan-lab/STRling-nf\n", - "525 ../../../Workflow-Corpus-Open-License/mtuong/nextflow-tychus\n", - "526 ../../../Workflow-Corpus-Open-License/UCL-BLIC/nf-ginkgo\n", - "527 ../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline\n", - "[10] Error in the file '../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/subworkflows/local/input_check.nf': Something went wrong in an include, possibly at line 5. No such file: '../../../Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/modules/local/samplesheet_check.nf'.\n", - "528 ../../../Workflow-Corpus-Open-License/connor-lab/qc_nextflow\n", - "529 ../../../Workflow-Corpus-Open-License/lconde-ucl/rnaseq_variant_calling\n", - "530 ../../../Workflow-Corpus-Open-License/lconde-ucl/wgsalign\n", - "531 ../../../Workflow-Corpus-Open-License/lconde-ucl/DGE\n", - "532 ../../../Workflow-Corpus-Open-License/lconde-ucl/runthis\n", - "533 ../../../Workflow-Corpus-Open-License/lconde-ucl/merge_fastq\n", - "534 ../../../Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-GFE\n", - "535 ../../../Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-OptiType\n", - "536 ../../../Workflow-Corpus-Open-License/FilipThorn/nf_mito-mania\n", - "537 ../../../Workflow-Corpus-Open-License/sheynkman-lab/Long-Read-Proteogenomics\n", - "538 ../../../Workflow-Corpus-Open-License/erikrikarddaniel/magmap\n", - "539 ../../../Workflow-Corpus-Open-License/erikrikarddaniel/pfitmap-nextflow\n", - "540 ../../../Workflow-Corpus-Open-License/genepi/nf-gwas\n", - "541 ../../../Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc/subworkflows/local/tidk.nf': 'set { ch_list_of_a_posteriori_tidk_plots }' is neither a process, subworkflow or an operator. In the executor 'ch_explored_repeat_seq\n", + "100 Workflow-Corpus-Open-License/edgano/TCoffee-NatureProtocol-nf\n", + "101 Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/montilab/nf-gwas-pipeline/gwas.nf': 'pcrelate' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "102 Workflow-Corpus-Open-License/montilab/shine-nf\n", + "103 Workflow-Corpus-Open-License/montilab/pipeliner-2\n", + "104 Workflow-Corpus-Open-License/mmolari/genome-assembly\n", + "105 Workflow-Corpus-Open-License/dfornika/cpo-pipeline-nextflow\n", + "106 Workflow-Corpus-Open-License/dfornika/depth-analysis-nextflow\n", + "107 Workflow-Corpus-Open-License/rbpisupati/nf-haplocaller\n", + "108 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/lyz-nf\n", + "109 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/demux-nf\n", + "110 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/NYU-Molecular-Pathology/NGS580-nf/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "111 Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/NYU-Molecular-Pathology/LG-PACT/main.nf': 'snp_pileup' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "112 Workflow-Corpus-Open-License/tomsing1/nf-tutorial-blast\n", + "113 Workflow-Corpus-Open-License/idfarbanecha/benchmark-MeSS-CAMISIM\n", + "114 Workflow-Corpus-Open-License/DHQP/SNVPhyl_Nextflow\n", + "115 Workflow-Corpus-Open-License/nibscbioinformatics/nf-core-bagobugs\n", + "116 Workflow-Corpus-Open-License/dchebotarov/nextflow-variant-calling\n", + "117 Workflow-Corpus-Open-License/HPCBio/16S-rDNA-dada2-pipeline\n", + "118 Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/SNU_2D_ProgrammingTools_IDE_NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", + "119 Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/Learn-NextFlow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", + "120 Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/seanpm2001/AI2001_Category-Source_Code-SC-Nextflow/LICENSE.nf': Not the same number of opening and closing parentheses '()' in the file.\n", + "121 Workflow-Corpus-Open-License/SamStudio8/elan-nextflow\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/SamStudio8/elan-nextflow/workflows/elan.nf': Not the same number of parameters given as input for the process 'announce_uploads', possibly at line 14.\n", + "122 Workflow-Corpus-Open-License/hnawar/nextflow-cloudrun\n", + "123 Workflow-Corpus-Open-License/robsyme/nf-repeatmasking\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/robsyme/nf-repeatmasking/main.nf': 'recentLTRs' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "124 Workflow-Corpus-Open-License/robsyme/markerdev\n", + "125 Workflow-Corpus-Open-License/TARGENE/targene-pipeline\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/TARGENE/targene-pipeline/workflows/targene.nf': The subworkflow 'SVPWorkflow' doesn't emit anything. It is given to an operation, possibly at line 71.\n", + "126 Workflow-Corpus-Open-License/Boehringer-Ingelheim/flowml-pipeline\n", + "127 Workflow-Corpus-Open-License/dgarrimar/mvgwas-nf\n", + "128 Workflow-Corpus-Open-License/dgarrimar/gemma-nf\n", + "129 Workflow-Corpus-Open-License/axelwalter/diametalyzer\n", + "130 Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline\n", + "[9] Error in the file 'Workflow-Corpus-Open-License/HSPH-QBRC/target-pipeline/pipeline.nf': A tuple is associated with an call, possibly at line 288. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", + "131 Workflow-Corpus-Open-License/oist/LuscombeU_Nextflow_Pipeline_Template\n", + "132 Workflow-Corpus-Open-License/jhayer/baargin\n", + "133 Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning\n", + "[9] Error in the file 'Workflow-Corpus-Open-License/JBris/nextflow-graph-machine-learning/gnn_pipeline.nf': A tuple is associated with an call, possibly at line 34. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.\n", + "134 Workflow-Corpus-Open-License/AndersenLab/ril-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/AndersenLab/ril-nf/main.nf': 'fq_coverage' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "135 Workflow-Corpus-Open-License/AndersenLab/alignment-nf\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/AndersenLab/alignment-nf/main.nf': '(coverage_id & idxstats_id & flagstat_id & stats_id)' is neither a process, subworkflow or an operator. In the executor 'alignment.out.map { row, bam, bai -> [\"id\", row.id, bam, bai ]} | (coverage_id & idxstats_id & flagstat_id & stats_id)'.\n", + "136 Workflow-Corpus-Open-License/AndersenLab/nil-ril-nf\n", + "137 Workflow-Corpus-Open-License/AndersenLab/sv-nf\n", + "138 Workflow-Corpus-Open-License/AndersenLab/cegwas2-nf\n", + "139 Workflow-Corpus-Open-License/MaestSi/UMInator\n", + "140 Workflow-Corpus-Open-License/MaestSi/CharONT2\n", + "141 Workflow-Corpus-Open-License/MaestSi/nf-m6anet\n", + "142 Workflow-Corpus-Open-License/MaestSi/pycoMethFlow\n", + "143 Workflow-Corpus-Open-License/MaestSi/ONTrack2\n", + "144 Workflow-Corpus-Open-License/phac-nml/mikrokondo\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/phac-nml/mikrokondo/main.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 87.\n", + "145 Workflow-Corpus-Open-License/lescailab/fenicsmpi\n", + "146 Workflow-Corpus-Open-License/Pooran-Dewari/SNP_array_nextflow\n", + "147 Workflow-Corpus-Open-License/Pooran-Dewari/Nextflow-pipeline-Extract-precise-location-of-gimme-maelstrom-TF-motifs\n", + "148 Workflow-Corpus-Open-License/lars20070/nextflow_lfq\n", + "149 Workflow-Corpus-Open-License/shaunchuah/cfdna_nextflow\n", + "150 Workflow-Corpus-Open-License/boulund/metagenome_pipeline\n", + "151 Workflow-Corpus-Open-License/PGScatalog/pgsc_calc\n", + "152 Workflow-Corpus-Open-License/ODiogoSilva/innuca-nf\n", + "153 Workflow-Corpus-Open-License/zamanianlab/Core_smRNAseq-nf\n", + "154 Workflow-Corpus-Open-License/sysbiomelab/meteor_pipeline\n", + "155 Workflow-Corpus-Open-License/lstevens17/nemAsm\n", + "156 Workflow-Corpus-Open-License/grst/minimal-nextflow-template\n", + "157 Workflow-Corpus-Open-License/grst/nextflow-notebook-pipeline\n", + "158 Workflow-Corpus-Open-License/grst/bd_rhapsody_velocyto\n", + "159 Workflow-Corpus-Open-License/grst/universal_analysis_pipeline\n", + "160 Workflow-Corpus-Open-License/friederhadlich/nextflow_ultraLowInput\n", + "161 Workflow-Corpus-Open-License/CDCgov/mycosnp-nf\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/CDCgov/mycosnp-nf/subworkflows/local/snpeff_build.nf': 'SNPEFF_BUILD' is expected to be defined in the file, but it could not be found.\n", + "162 Workflow-Corpus-Open-License/CDCgov/tostadas\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/CDCgov/tostadas/workflows/tostadas.nf': Not the same number of parameters given as input for the process 'UPDATE_SUBMISSION', possibly at line 203.\n", + "163 Workflow-Corpus-Open-License/MarieLataretu/nextflow-mwe\n", + "164 Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/workflows/spatial.nf': Something went wrong in an include, possibly at line 46. No such file: 'Workflow-Corpus-Open-License/break-through-cancer/btc-spatial-pipelines/modules/bayestme/nextflow/subworkflows/bayestme/bayestme_basic_visium_analysis/main.nf'.\n", + "165 Workflow-Corpus-Open-License/SarahMaman/NextflowRNAseq\n", + "166 Workflow-Corpus-Open-License/angelovangel/nxf-kraken2\n", + "167 Workflow-Corpus-Open-License/cbcrg/msa-af2-nf\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/cbcrg/msa-af2-nf/main.nf': The call for 'run_seq_aln' coudn't be found, before its use in the operation 'run_seq_aln.out.seq_aln_output.combine(run_psicoffee.out.psicoffee_output, by: 0).combine(dssp_to_fasta.out.dssp_output, by: 0).combine(run_struct_aln.out.struct_output, by: 0).combine(templates, by: 0).combine(structures, by: 0).combine(run_alphafold2.out.af2_models.groupTuple(), by: 0).set{comp_and_eval_input}', possibly at line 73. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "168 Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/cbcrg/nf-phdcourse20/rnaseq-flow.nf': No 'main' workflow was found.\n", + "169 Workflow-Corpus-Open-License/cbcrg/nf-phdcourse19\n", + "170 Workflow-Corpus-Open-License/cbcrg/nf-phdcourse21\n", + "171 Workflow-Corpus-Open-License/cloud303-kloucks/nextflow-debugging\n", + "172 Workflow-Corpus-Open-License/noamteyssier/pipseq_nextflow\n", + "173 Workflow-Corpus-Open-License/noamteyssier/10x_rna_velocity_nextflow\n", + "174 Workflow-Corpus-Open-License/noamteyssier/sciseq_rna_velocity_nextflow\n", + "175 Workflow-Corpus-Open-License/uct-cbio/bacterial_variant_calling\n", + "176 Workflow-Corpus-Open-License/ameynert/nf-indelible\n", + "177 Workflow-Corpus-Open-License/OtimusOne/AFPAP\n", + "178 Workflow-Corpus-Open-License/nf-wrap/main\n", + "179 Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/TheJacksonLaboratory/cs-nf-pipelines/subworkflows/hs_pta.nf': The call for 'PICARD_MARKDUPLICATES' coudn't be found, before its use in the operation 'apply_bqsr = PICARD_MARKDUPLICATES.out.dedup_bam.join(GATK_BASERECALIBRATOR.out.table)', possibly at line 175. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "180 Workflow-Corpus-Open-License/TheJacksonLaboratory/nextflow-sra-cloud\n", + "181 Workflow-Corpus-Open-License/TheJacksonLaboratory/pdx-nextflow\n", + "182 Workflow-Corpus-Open-License/TheJacksonLaboratory/crf_nextflow_basics\n", + "183 Workflow-Corpus-Open-License/TheJacksonLaboratory/ChIA-PIPE_nextflow\n", + "184 Workflow-Corpus-Open-License/TheJacksonLaboratory/mmrSVD\n", + "185 Workflow-Corpus-Open-License/evanfloden/stable-diffusion-nf\n", + "186 Workflow-Corpus-Open-License/evanfloden/nf-module-demo\n", + "187 Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/SLU-AMB/read-preprocessing/main.nf': No 'main' workflow was found.\n", + "188 Workflow-Corpus-Open-License/HealthInnovationEast/cgpwgs-nf\n", + "189 Workflow-Corpus-Open-License/HealthInnovationEast/ExpansionHunter\n", + "190 Workflow-Corpus-Open-License/becavin-lab/nf-blast\n", + "191 Workflow-Corpus-Open-License/rsuchecki/nextflow-walkthrough\n", + "192 Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules/bacteria-example.nf': No 'main' workflow was found.\n", + "193 Workflow-Corpus-Open-License/FischbachLab/nf-reads-profiler\n", + "194 Workflow-Corpus-Open-License/FischbachLab/nf-blast\n", + "195 Workflow-Corpus-Open-License/utia-gc/ngs\n", + "196 Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-template\n", + "197 Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-wf-megSAP\n", + "198 Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-rnaseq\n", + "199 Workflow-Corpus-Open-License/JacobLay/NextflowIntro\n", + "200 Workflow-Corpus-Open-License/OpenMSConsulting/NextflowLFQ\n", + "201 Workflow-Corpus-Open-License/vibbits/chipseq-nextflow\n", + "202 Workflow-Corpus-Open-License/OlgaChern/nextflow_gentrius_sim\n", + "203 Workflow-Corpus-Open-License/bkohrn/picard_demux_nextflow\n", + "204 Workflow-Corpus-Open-License/manuelesimi/hello-nextflow\n", + "205 Workflow-Corpus-Open-License/kkerns85/midas_nf_tower\n", + "206 Workflow-Corpus-Open-License/microgenlab/porefile\n", + "207 Workflow-Corpus-Open-License/open2c/distiller-nf\n", + "208 Workflow-Corpus-Open-License/MiGurke/nfmap\n", + "209 Workflow-Corpus-Open-License/MiGurke/nfvacal\n", + "210 Workflow-Corpus-Open-License/MiGurke/nfcongeneus\n", + "211 Workflow-Corpus-Open-License/tluquez/QUARS\n", + "212 Workflow-Corpus-Open-License/zhanyinx/metagenomics\n", + "213 Workflow-Corpus-Open-License/aertslab/SpatialNF\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/aertslab/SpatialNF/main.nf': No 'main' workflow was found.\n", + "214 Workflow-Corpus-Open-License/aertslab/scenic-nf\n", + "215 Workflow-Corpus-Open-License/systems-genomics-lab/next-bgc\n", + "216 Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert/modules/processes.nf': Multiple 'input:' were found in the process 'Convert_EachFileFromRoot2SeparateOMETIFF'.\n", + "217 Workflow-Corpus-Open-License/bioShaun/om-nf-prepare\n", + "218 Workflow-Corpus-Open-License/bioShaun/xms-rnaseq-nf\n", + "219 Workflow-Corpus-Open-License/lepsalex/nextflow-pcawg-bwa-mem-workflow\n", + "220 Workflow-Corpus-Open-License/HadrienG/nanoflow\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/HadrienG/nanoflow/main.nf': 'assembly' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "221 Workflow-Corpus-Open-License/HadrienG/nextflow_rna\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/HadrienG/nextflow_rna/rna.nf': No 'main' workflow was found.\n", + "222 Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/crukci-bioinformatics/nextflow-support/functions.nf': No 'main' workflow was found.\n", + "223 Workflow-Corpus-Open-License/hoelzer/nf-hmmsearch\n", + "224 Workflow-Corpus-Open-License/hoelzer/dammit-nf\n", + "225 Workflow-Corpus-Open-License/hoelzer/virify\n", + "226 Workflow-Corpus-Open-License/peterk87/nf-flu\n", + "227 Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/EBI-Metagenomics/emg-viral-pipeline/virify.nf': Not the same number of parameters given as input for the subworklfow 'annotate' in the call, possibly at line 649.\n", + "228 Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/cidgoh/nf-ncov-voc/modules/local/custom.nf': Multiple 'output:' were found in the process 'processGVCF'?\n", + "229 Workflow-Corpus-Open-License/jagedn/nextflow-groogle-sheet\n", + "230 Workflow-Corpus-Open-License/B-UMMI/DEN-IM\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/B-UMMI/DEN-IM/DEN-IM.nf': 'compile_status_buffer' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "231 Workflow-Corpus-Open-License/openproblems-bio/openproblems-v2\n", + "232 Workflow-Corpus-Open-License/PRIDE-Archive/pride-molecule-indexer\n", + "233 Workflow-Corpus-Open-License/DaneVass/BARtab\n", + "234 Workflow-Corpus-Open-License/LeoniePohl/nextflow-diffexp-testpipeline\n", + "235 Workflow-Corpus-Open-License/stenglein-lab/viral_variant_caller\n", + "236 Workflow-Corpus-Open-License/jemunro/Tidy-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/jemunro/Tidy-nf/example.nf': No 'main' workflow was found.\n", + "237 Workflow-Corpus-Open-License/mattfemia/scrnaseq-pipeline\n", + "238 Workflow-Corpus-Open-License/MHH-RCUG/nf_wochenende\n", + "239 Workflow-Corpus-Open-License/DarianHole/test-nextflow\n", + "240 Workflow-Corpus-Open-License/fmalmeida/MpGAP\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/fmalmeida/MpGAP/workflows/hybrid.nf': Multiple 'main:' were found in the subworkflow 'HYBRID'.\n", + "241 Workflow-Corpus-Open-License/fmalmeida/bacannot\n", + "242 Workflow-Corpus-Open-License/uel3/UnO_nf\n", + "243 Workflow-Corpus-Open-License/nttg8100/Simple-RNA-seq-Nextflow-with-Salmon\n", + "244 Workflow-Corpus-Open-License/fredjaya/msmc-nf\n", + "245 Workflow-Corpus-Open-License/pgonzale60/nxf_pipelines\n", + "246 Workflow-Corpus-Open-License/noepozzan/small-peptide-pipeline\n", + "247 Workflow-Corpus-Open-License/lukfor/pgs-calc-nf\n", + "248 Workflow-Corpus-Open-License/biocorecrg/contamination-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/biocorecrg/contamination-nf/main.nf': Not the same number of opening and closing curlies '{}' in the file.\n", + "249 Workflow-Corpus-Open-License/biocorecrg/nf-cloud-gpu-test\n", + "250 Workflow-Corpus-Open-License/biocorecrg/MOP2\n", + "251 Workflow-Corpus-Open-License/biocorecrg/nextflow_detached_db_wrapper\n", + "252 Workflow-Corpus-Open-License/NCBI-Hackathons/ATACFlow\n", + "253 Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/NCBI-Hackathons/SPeW/align.nf': Not the same number of opening and closing curlies '{}' in the file.\n", + "254 Workflow-Corpus-Open-License/breichholf/smRNAseq\n", + "255 Workflow-Corpus-Open-License/nextflow-io/cwl2nxf\n", + "256 Workflow-Corpus-Open-License/nextflow-io/nf-ffq\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/nextflow-io/nf-ffq/ffq.nf': No 'main' workflow was found.\n", + "257 Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/main.nf': Something went wrong in an include, possibly at line 76. No such file: 'Workflow-Corpus-Open-License/nextflow-io/elixir-workshop-21/${subwork_folder}/fastqc.nf'.\n", + "258 Workflow-Corpus-Open-License/nextflow-io/gccbosc18-training\n", + "259 Workflow-Corpus-Open-License/nextflow-io/socks\n", + "260 Workflow-Corpus-Open-License/JackCurragh/Nextflow-Template\n", + "261 Workflow-Corpus-Open-License/ZuberLab/mageck-nf\n", + "262 Workflow-Corpus-Open-License/ZuberLab/vbcf-nf\n", + "263 Workflow-Corpus-Open-License/ZuberLab/crispr-mageck-nf\n", + "264 Workflow-Corpus-Open-License/ZuberLab/guidemapper-nf\n", + "265 Workflow-Corpus-Open-License/ZuberLab/crispr-process-nf\n", + "266 Workflow-Corpus-Open-License/ZuberLab/crispr-nf\n", + "267 Workflow-Corpus-Open-License/ZuberLab/sra-nf\n", + "268 Workflow-Corpus-Open-License/oxfordfun/FunSnippy\n", + "269 Workflow-Corpus-Open-License/mmatthews06/nextflow-playground\n", + "270 Workflow-Corpus-Open-License/ricomnl/bioinformatics-pipeline-tutorial\n", + "271 Workflow-Corpus-Open-License/dolphinnext/rnaseq\n", + "272 Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: 'Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'.\n", + "273 Workflow-Corpus-Open-License/hoelzer-lab/rnaflow\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/hoelzer-lab/rnaflow/main.nf': 'sortmerna' is trying to be created as a channel, possibly at line 475. It already exists as a process or a subworkflow in the nextflow file.\n", + "274 Workflow-Corpus-Open-License/isugifNF/blast\n", + "275 Workflow-Corpus-Open-License/vmikk/BatchBlaster\n", + "276 Workflow-Corpus-Open-License/vmikk/PhyloNext\n", + "277 Workflow-Corpus-Open-License/bschiffthaler/nf-modules\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/bschiffthaler/nf-modules/multiqc.nf': No 'main' workflow was found.\n", + "278 Workflow-Corpus-Open-License/pcrxn/ProkkaFlow\n", + "279 Workflow-Corpus-Open-License/alneberg/trigger_error_nf\n", + "280 Workflow-Corpus-Open-License/opencobra/jeweler\n", + "281 Workflow-Corpus-Open-License/faithman/variant-nf\n", + "282 Workflow-Corpus-Open-License/digenoma-lab/nf-groot\n", + "283 Workflow-Corpus-Open-License/digenoma-lab/k-count-nf\n", + "284 Workflow-Corpus-Open-License/ATpoint/nf_findMotifs\n", + "285 Workflow-Corpus-Open-License/eQTL-Catalogue/colocalisation\n", + "286 Workflow-Corpus-Open-License/eQTL-Catalogue/susie-workflow\n", + "287 Workflow-Corpus-Open-License/veidenberg/tools-api-nextflow\n", + "288 Workflow-Corpus-Open-License/RibosomeCRCL/ribomethseq-nf\n", + "289 Workflow-Corpus-Open-License/anajung/CZI_addon\n", + "290 Workflow-Corpus-Open-License/cometsong/gbrs_nxf\n", + "291 Workflow-Corpus-Open-License/cometsong/ATAC_Seq_nxf\n", + "292 Workflow-Corpus-Open-License/jvierstra/nf-rnaseq\n", + "293 Workflow-Corpus-Open-License/RHReynolds/mkfastq\n", + "294 Workflow-Corpus-Open-License/bactopia/bactopia\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/bactopia/bactopia/workflows/teton.nf': Something went wrong in an include, possibly at line 33. No such file: 'Workflow-Corpus-Open-License/bactopia/bactopia/modules/local/bactopia/gather_samples/main.nf'.\n", + "295 Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/DLBPointon/HymenopteraAnalysis/modules/nf-core/modules/blast/makeblastdb/main.nf': 'SIGS_BLAST_MAKEBLASTDB' is expected to be defined in the file, but it could not be found.\n", + "296 Workflow-Corpus-Open-License/tiagofilipe12/pATLASflow\n", + "297 Workflow-Corpus-Open-License/usafsam/mad_river_wf\n", + "298 Workflow-Corpus-Open-License/sebgoti/spatial-pipeline\n", + "299 Workflow-Corpus-Open-License/esteinig/nf-mvp\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/esteinig/nf-mvp/lib/utils.nf': 'getSubsampleReads' is expected to be defined in the file, but it could not be found.\n", + "300 Workflow-Corpus-Open-License/cedarwarman/pollen_cv_nextflow\n", + "301 Workflow-Corpus-Open-License/lehtiolab/nf-msconvert\n", + "302 Workflow-Corpus-Open-License/lehtiolab/ddamsproteomics\n", + "303 Workflow-Corpus-Open-License/stajichlab/nf-comparative-genomics\n", + "304 Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/vib-singlecell-nf/vsn-pipelines/main.nf': No 'main' workflow was found.\n", + "305 Workflow-Corpus-Open-License/oalmelid/lift-over-nf\n", + "306 Workflow-Corpus-Open-License/dmalzl/howto-nf\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/dmalzl/howto-nf/workflows/chipseq.nf': 'CHIPSEQ' is expected to be defined in the file, but it could not be found.\n", + "307 Workflow-Corpus-Open-License/eastgenomics/mutect2_nextflow\n", + "308 Workflow-Corpus-Open-License/eastgenomics/VerifyBamID_nextflow\n", + "309 Workflow-Corpus-Open-License/BU-ISCIII/bacterial_assembly-nf\n", + "310 Workflow-Corpus-Open-License/BU-ISCIII/panelLowFreq-nf\n", + "311 Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/BU-ISCIII/bacterial_wgs_training/main.nf': 'srst2_resistance' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "312 Workflow-Corpus-Open-License/AllenInstitute/deepinterpolation_nextflow\n", + "313 Workflow-Corpus-Open-License/sergpolly/random-nextflow-utils\n", + "314 Workflow-Corpus-Open-License/CIBERER-pipelines/mosaicism_nextflow\n", + "315 Workflow-Corpus-Open-License/EnriqueDoster/bioinformatic-nextflow-pipelines\n", + "316 Workflow-Corpus-Open-License/AlfredUg/QuasiFlow\n", + "317 Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-model2data\n", + "318 Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synstage\n", + "319 Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synindex\n", + "320 Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-genie\n", + "321 Workflow-Corpus-Open-License/vntasis/stan-nf\n", + "322 Workflow-Corpus-Open-License/maxibor/kraken-nf\n", + "323 Workflow-Corpus-Open-License/maxibor/organdiet\n", + "324 Workflow-Corpus-Open-License/nkrumm/hello\n", + "325 Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/Schaudge/nextflow-in-practice/somatic_vardict_pindel.nf': Multiple 'when:' were found in the process 'cnv_oncocnv_tumor_controls'.\n", + "326 Workflow-Corpus-Open-License/GunzIvan28/nextflow-rMAP-devt\n", + "327 Workflow-Corpus-Open-License/CCBR/CHAMPAGNE\n", + "328 Workflow-Corpus-Open-License/CCBR/CCBR_NextflowTemplate\n", + "329 Workflow-Corpus-Open-License/gleisonm/nextflow_bigscape\n", + "330 Workflow-Corpus-Open-License/aws-samples/aws-gatk-recipe-nextflow-pipeline\n", + "331 Workflow-Corpus-Open-License/thanhleviet/nextflow-ratt\n", + "332 Workflow-Corpus-Open-License/transXpress/transXpress-nextflow\n", + "333 Workflow-Corpus-Open-License/marc-jones/nextflow-example\n", + "334 Workflow-Corpus-Open-License/kenibrewer/shapeseq\n", + "335 Workflow-Corpus-Open-License/kenibrewer/simplenextflow\n", + "336 Workflow-Corpus-Open-License/gwright99/hello-nonmain\n", + "337 Workflow-Corpus-Open-License/jtmccr1/beast_analysis\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/jtmccr1/beast_analysis/beast_analysis.nf': Multiple 'input:' were found in the process 'mcc'.\n", + "338 Workflow-Corpus-Open-License/crashGoBoom/nf-video\n", + "339 Workflow-Corpus-Open-License/Dowell-Lab/RNAseq-Flow\n", + "340 Workflow-Corpus-Open-License/Dowell-Lab/Bidirectional-Flow\n", + "341 Workflow-Corpus-Open-License/Dowell-Lab/Analysis-Flow\n", + "342 Workflow-Corpus-Open-License/Dowell-Lab/ChIP-Flow\n", + "343 Workflow-Corpus-Open-License/bguo068/snp_call_nf\n", + "344 Workflow-Corpus-Open-License/bguo068/posseleff_empirical\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/bguo068/posseleff_empirical/01_filter_vcf.nf': Not the same number of parameters given as input for the process 'BCFTOOLS_VIEW_FILTER_SAMPLE_BY_IMISS1', possibly at line 165.\n", + "345 Workflow-Corpus-Open-License/salzman-lab/SpliZ\n", + "346 Workflow-Corpus-Open-License/KohlbacherLab/nextflow-clinvap\n", + "347 Workflow-Corpus-Open-License/ChrisgKent/flye-on-cluster\n", + "348 Workflow-Corpus-Open-License/RenneLab/CnR-flow\n", + "349 Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/TalusBio/nf-encyclopedia/subworkflows/encyclopedia.nf': 'set { global_files }' is neither a process, subworkflow or an operator. In the executor 'Channel.empty() | set { global_files }', possibly at line 89.\n", + "350 Workflow-Corpus-Open-License/shenwei356/blast-nf\n", + "351 Workflow-Corpus-Open-License/ralsallaq/metaGx_nf\n", + "352 Workflow-Corpus-Open-License/ikmb-denbi/genome-annotation\n", + "353 Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/AusSRC/WALLABY_pipelines/main.nf': Not the same number of opening and closing parentheses '()' in the file.\n", + "354 Workflow-Corpus-Open-License/sauriiiin/rnaseeker\n", + "355 Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/NBISweden/K9-WGS-Pipeline/main.nf': 'hardfilters_snp' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "356 Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/NBISweden/pipelines-nextflow/subworkflows/abinitio_training/main.nf': Not the same number of parameters given as input for the process 'BLAST_BLASTP', possibly at line 54.\n", + "357 Workflow-Corpus-Open-License/FloWuenne/nextflow_saige_dsl2\n", + "358 Workflow-Corpus-Open-License/FloWuenne/meta-METAL_nextflow_dsl2\n", + "359 Workflow-Corpus-Open-License/olgabot/nextflow-test-aws\n", + "360 Workflow-Corpus-Open-License/heuermh/minnebar15-workflow\n", + "361 Workflow-Corpus-Open-License/kviljoen/uct-srst2\n", + "362 Workflow-Corpus-Open-License/kviljoen/EMIRGE_nextflow\n", + "363 Workflow-Corpus-Open-License/tuzov/nf-cg-helloworld\n", + "364 Workflow-Corpus-Open-License/t-neumann/salmon-nf\n", + "365 Workflow-Corpus-Open-License/FredHutch/souper-star\n", + "366 Workflow-Corpus-Open-License/FredHutch/VMAA\n", + "367 Workflow-Corpus-Open-License/FredHutch/workflow-template-nextflow\n", + "368 Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/shreyasanjay22/NextflowPipeline/rnaseq_script.nf': No 'main' workflow was found.\n", + "369 Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_4\n", + "370 Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1_print_hello_world\n", + "371 Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1\n", + "372 Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_5\n", + "373 Workflow-Corpus-Open-License/danielecook/nextflow-tutorial\n", + "374 Workflow-Corpus-Open-License/rnajena/RNAswarm\n", + "375 Workflow-Corpus-Open-License/tdelhomme/vcf_ancestry-nf\n", + "376 Workflow-Corpus-Open-License/tdelhomme/SimulateLowCovSeq-nf\n", + "377 Workflow-Corpus-Open-License/tdelhomme/variantfiltering-nf\n", + "378 Workflow-Corpus-Open-License/tdelhomme/RegionalEnrichment-nf\n", + "379 Workflow-Corpus-Open-License/tdelhomme/SV-simulation-nf\n", + "380 Workflow-Corpus-Open-License/PavriLab/repliseq-nf\n", + "381 Workflow-Corpus-Open-License/PavriLab/geneIS-nf\n", + "382 Workflow-Corpus-Open-License/PavriLab/hicer-nf\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/PavriLab/hicer-nf/workflows/hicer.nf': To much to unpack : The subworkflow 'PREPARE_GENOME' emits over one channel in a operation, possibly at line 146.\n", + "383 Workflow-Corpus-Open-License/gp201/Freyja_pathogen_workflow_alpha\n", + "384 Workflow-Corpus-Open-License/IARCbioinfo/LiftOver-nf\n", + "385 Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/IARCbioinfo/nf_coverage_demo/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file.\n", + "386 Workflow-Corpus-Open-License/IARCbioinfo/TCGA_platypus-nf\n", + "387 Workflow-Corpus-Open-License/IARCbioinfo/CODEX-nf\n", + "388 Workflow-Corpus-Open-License/IARCbioinfo/purple-nf\n", + "389 Workflow-Corpus-Open-License/IARCbioinfo/table_annovar-nf\n", + "390 Workflow-Corpus-Open-License/IARCbioinfo/octopus-nf\n", + "391 Workflow-Corpus-Open-License/IARCbioinfo/damage-estimator-nf\n", + "392 Workflow-Corpus-Open-License/IARCbioinfo/NGSCheckMate-nf\n", + "393 Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/IARCbioinfo/gene-fusions-nf/main.nf': 'arriba' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "394 Workflow-Corpus-Open-License/IARCbioinfo/gatk4-DataPreProcessing-nf\n", + "395 Workflow-Corpus-Open-License/IARCbioinfo/template-nf\n", + "396 Workflow-Corpus-Open-License/IARCbioinfo/ampliconarchitect-nf\n", + "397 Workflow-Corpus-Open-License/IARCbioinfo/bamsurgeon-nf\n", + "398 Workflow-Corpus-Open-License/IARCbioinfo/BQSR-nf\n", + "399 Workflow-Corpus-Open-License/jianhong/universalModule\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/jianhong/universalModule/chipseq.nf': Something went wrong in an include, possibly at line 14. No such file: 'Workflow-Corpus-Open-License/jianhong/universalModule/loadModule(checksum,.nf'.\n", + "400 Workflow-Corpus-Open-License/jianhong/nextflowTutorial\n", + "401 Workflow-Corpus-Open-License/likelet/ExomePipe\n", + "402 Workflow-Corpus-Open-License/bentsherman/tesseract\n", + "403 Workflow-Corpus-Open-License/BCCDC-PHL/dragonflye-nf\n", + "404 Workflow-Corpus-Open-License/BCCDC-PHL/covflo\n", + "405 Workflow-Corpus-Open-License/BCCDC-PHL/fluflo\n", + "406 Workflow-Corpus-Open-License/bhargava-morampalli/cdnaseqont-nextflow\n", + "407 Workflow-Corpus-Open-License/pandora414/ssnp\n", + "408 Workflow-Corpus-Open-License/pandora414/lncRNA\n", + "409 Workflow-Corpus-Open-License/austinreidmanny/tvv-nf\n", + "410 Workflow-Corpus-Open-License/stevekm/nextflow-communicator\n", + "411 Workflow-Corpus-Open-License/stevekm/newfile-detector-nf\n", + "412 Workflow-Corpus-Open-License/keoughkath/GBGCnf\n", + "413 Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/wassermanlab/Variant_catalogue_pipeline/subworkflow/SNV.nf': 'SNV' is trying to be created as a channel, possibly at line 27. It already exists as a process or a subworkflow in the nextflow file.\n", + "414 Workflow-Corpus-Open-License/team113sanger/t113_irods_to_lustre\n", + "415 Workflow-Corpus-Open-License/BrianLohman/pdx-nf\n", + "416 Workflow-Corpus-Open-License/BrianLohman/ctseq-nf\n", + "417 Workflow-Corpus-Open-License/BrianLohman/RNAseq-variant-calling-nf\n", + "418 Workflow-Corpus-Open-License/BrianLohman/cellranger-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/BrianLohman/cellranger-nf/main.nf': An odd number of '\"\"\"' was found in the code.\n", + "419 Workflow-Corpus-Open-License/WarrenLab/longread-polish-nf\n", + "420 Workflow-Corpus-Open-License/WarrenLab/longread-svs-nf\n", + "421 Workflow-Corpus-Open-License/WarrenLab/shortread-polish-nf\n", + "422 Workflow-Corpus-Open-License/WarrenLab/purge-haplotigs-nf\n", + "423 Workflow-Corpus-Open-License/WarrenLab/minigraph-cactus-nf\n", + "424 Workflow-Corpus-Open-License/WarrenLab/cellranger-nf\n", + "425 Workflow-Corpus-Open-License/WarrenLab/hic-scaffolding-nf\n", + "426 Workflow-Corpus-Open-License/limrp/nextflow_metagenomics\n", + "427 Workflow-Corpus-Open-License/limrp/nextflow_subworkflow\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/limrp/nextflow_subworkflow/subworkflows/local/fasta_metaprodigal_cdhit.nf': Not the same number of parameters given as input for the process 'PRODIGAL', possibly at line 21.\n", + "428 Workflow-Corpus-Open-License/zajakin/sRNAflow\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/zajakin/sRNAflow/sRNAflow.nf': No 'main' workflow was found.\n", + "429 Workflow-Corpus-Open-License/seqeralabs/nf-canary\n", + "430 Workflow-Corpus-Open-License/arontommi/RNAseq-VAX\n", + "431 Workflow-Corpus-Open-License/ObenaufLab/snv-calling-nf\n", + "432 Workflow-Corpus-Open-License/ObenaufLab/sv-calling-nf\n", + "433 Workflow-Corpus-Open-License/ObenaufLab/virus-detection-nf\n", + "434 Workflow-Corpus-Open-License/Streit-lab/enhancer_annotation_and_motif_analysis\n", + "435 Workflow-Corpus-Open-License/kullrich/snpless-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/kullrich/snpless-nf/main.nf': 'genmap' is trying to be created as a channel, possibly at line 263. It already exists as a process or a subworkflow in the nextflow file.\n", + "436 Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/BPHL-Molecular/Sanibel/flaq_amr_plus2.nf': Not the same number of parameters given as input for the process 'plusAnalyses'.\n", + "437 Workflow-Corpus-Open-License/PAIN-initiative/nextflow-scRNAseq\n", + "438 Workflow-Corpus-Open-License/Ratoncito/callingcards\n", + "439 Workflow-Corpus-Open-License/x-kiana/nextflow_pipeline\n", + "440 Workflow-Corpus-Open-License/cellgeni/nf-workshop\n", + "441 Workflow-Corpus-Open-License/cellgeni/rnaseq\n", + "442 Workflow-Corpus-Open-License/cellgeni/scmapIndex\n", + "443 Workflow-Corpus-Open-License/evotools/nSPECTRa\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/evotools/nSPECTRa/include/workflow/mutyper.nf': 'chromosomeList' is trying to be created as a channel, possibly at line 10. It already exists as a process or a subworkflow in the nextflow file.\n", + "444 Workflow-Corpus-Open-License/evotools/nf-LO\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/evotools/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found.\n", + "445 Workflow-Corpus-Open-License/Sydney-Informatics-Hub/fastqc-nf\n", + "446 Workflow-Corpus-Open-License/Sydney-Informatics-Hub/bamQC-nf\n", + "447 Workflow-Corpus-Open-License/Sydney-Informatics-Hub/Germline-StructuralV-nf\n", + "448 Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/yash-puligundla/samtools-head-nf/main.nf': No 'main' workflow was found.\n", + "449 Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/main.nf': Something went wrong in an include, possibly at line 68. No such file: 'Workflow-Corpus-Open-License/jaumereig/geneidBLASTx-nf/${subwork_folder}/tools.nf'.\n", + "450 Workflow-Corpus-Open-License/mlf-core/nextflow-lcep\n", + "451 Workflow-Corpus-Open-License/wbazant/nextflow-hello-dsl2\n", + "452 Workflow-Corpus-Open-License/palfalvi/rnaseq\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/palfalvi/rnaseq/main.nf': The call for 'run_fastSE_qc' coudn't be found, before its use in the operation 'salmon_quantSE.out.collect().concat(run_fastSE_qc.out.collect())', possibly at line 217. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "453 Workflow-Corpus-Open-License/samlhao/nf-core-abricate\n", + "454 Workflow-Corpus-Open-License/samlhao/hgtsimulation\n", + "455 Workflow-Corpus-Open-License/samlhao/nextflow-spid\n", + "456 Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/MrOlm/nf-genomeresolvedmetagenomics/main.nf': No 'main' workflow was found.\n", + "457 Workflow-Corpus-Open-License/robomics/generate_higlass_gene_track\n", + "458 Workflow-Corpus-Open-License/alexthiery/modify-gtf\n", + "459 Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/raimondsre/population_scale_wgs_nextflow/main.nf': 'PCA' is trying to be created as a channel, possibly at line 1. It already exists as a process or a subworkflow in the nextflow file.\n", + "460 Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/sanger-bentley-group/GBS-Typer-sanger-nf/main.nf': Not the same number of parameters given as input for the process 'freebayes', possibly at line 159.\n", + "461 Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/sanger-bentley-group/gps-pipeline/modules/messages.nf': 'startMessage' is expected to be defined in the file, but it could not be found.\n", + "462 Workflow-Corpus-Open-License/mpieva/quicksand\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/mpieva/quicksand/workflows/00_setup.nf': 'setup' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file.\n", + "463 Workflow-Corpus-Open-License/Mxrcon/Savio_alignments_nf\n", + "464 Workflow-Corpus-Open-License/csiro-crop-informatics/repset\n", + "465 Workflow-Corpus-Open-License/csiro-crop-informatics/nextflow-embl-abr-webinar\n", + "466 Workflow-Corpus-Open-License/mhebrard/TrimFlow\n", + "467 Workflow-Corpus-Open-License/jowkar/xenocell_nextflow\n", + "468 Workflow-Corpus-Open-License/tthyer/nextflow-scratch\n", + "469 Workflow-Corpus-Open-License/julesjacobsen/nextflow-test\n", + "470 Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/soulj/SkeletalVis-SingleCell/main.nf': Not the same number of parameters given as input for the process 'ENA_DOWNLOAD', possibly at line 123.\n", + "471 Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/haniffalab/webatlas-pipeline/main.nf': No 'main' workflow was found.\n", + "472 Workflow-Corpus-Open-License/bts76-pitt/BCR_nextflow\n", + "473 Workflow-Corpus-Open-License/dnieuw/ENA_SARS_Cov2_nanopore\n", + "474 Workflow-Corpus-Open-License/nf-modules-hub/mykrobe\n", + "475 Workflow-Corpus-Open-License/nf-modules-hub/tb-profiler\n", + "476 Workflow-Corpus-Open-License/nf-modules-hub/mtbseq\n", + "477 Workflow-Corpus-Open-License/nf-modules-hub/gzip\n", + "478 Workflow-Corpus-Open-License/nf-modules-hub/snippy\n", + "479 Workflow-Corpus-Open-License/nf-modules-hub/trimmomatic\n", + "480 Workflow-Corpus-Open-License/nf-modules-hub/rd-analyzer\n", + "481 Workflow-Corpus-Open-License/nf-modules-hub/prokka\n", + "482 Workflow-Corpus-Open-License/nf-modules-hub/spotyping\n", + "483 Workflow-Corpus-Open-License/nf-modules-hub/kvarq\n", + "484 Workflow-Corpus-Open-License/nf-modules-hub/multiqc\n", + "485 Workflow-Corpus-Open-License/nf-modules-hub/nextflow_hub_process\n", + "486 Workflow-Corpus-Open-License/nf-modules-hub/quast\n", + "487 Workflow-Corpus-Open-License/nf-modules-hub/spades\n", + "488 Workflow-Corpus-Open-License/nf-modules-hub/rclone\n", + "489 Workflow-Corpus-Open-License/nf-modules-hub/fastqc\n", + "490 Workflow-Corpus-Open-License/mja/ukb-release-nf\n", + "491 Workflow-Corpus-Open-License/asereewit/rsv_ampseq\n", + "492 Workflow-Corpus-Open-License/scilus/dmriqc_flow\n", + "493 Workflow-Corpus-Open-License/RenzoTale88/nf-LO\n", + "[18] Error in the file 'Workflow-Corpus-Open-License/RenzoTale88/nf-LO/modules/processes/blat.nf': 'blat_custom' is expected to be defined in the file, but it could not be found.\n", + "494 Workflow-Corpus-Open-License/khigashi1987/CUTRUN_Nextflow\n", + "495 Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/walkercreek/subworkflows/local/preprocessing_read_qc.nf': Multiple 'emit:' were found in the subworkflow 'PREPROCESSING_READ_QC'. \n", + "496 Workflow-Corpus-Open-License/UPHL-BioNGS/Nextstrain_Build\n", + "497 Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Cecret/subworkflows/msa.nf': 'msa' is trying to be created as a channel, possibly at line 7. It already exists as a process or a subworkflow in the nextflow file.\n", + "498 Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Donut_Falls/workflows/assembly.nf': 'assembly' is trying to be created as a channel, possibly at line 11. It already exists as a process or a subworkflow in the nextflow file.\n", + "499 Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/UPHL-BioNGS/Grandeur/subworkflows/average_nucleotide_identity.nf': 'datasets_summary' is trying to be created as a channel, possibly at line 6. It already exists as a process or a subworkflow in the nextflow file.\n", + "500 Workflow-Corpus-Open-License/jallen73/teloSealer\n", + "501 Workflow-Corpus-Open-License/sidorov-si/nextflow-example-start\n", + "502 Workflow-Corpus-Open-License/gongyh/nf-core-scp\n", + "503 Workflow-Corpus-Open-License/gongyh/nf-core-scgs\n", + "504 Workflow-Corpus-Open-License/ikmb/nf-template\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/ikmb/nf-template/main.nf': Not the same number of parameters given as input for the subworklfow 'MAIN' in the call, possibly at line 38.\n", + "505 Workflow-Corpus-Open-License/ikmb/gwas-qc\n", + "506 Workflow-Corpus-Open-License/ikmb/gwas-assoc\n", + "507 Workflow-Corpus-Open-License/ikmb/finemapping\n", + "508 Workflow-Corpus-Open-License/ikmb/TOFU-MAaPO\n", + "509 Workflow-Corpus-Open-License/h3abionet/TADA\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/h3abionet/TADA/main.nf': Multiple 'when:' were found in the process 'ToQIIME2Aln'.\n", + "510 Workflow-Corpus-Open-License/phue/GWAS-nf\n", + "511 Workflow-Corpus-Open-License/athbaltzis/paralogs-nf\n", + "512 Workflow-Corpus-Open-License/athbaltzis/diff-AS-nf\n", + "513 Workflow-Corpus-Open-License/apeltzer/IGCG-featureCounts\n", + "514 Workflow-Corpus-Open-License/Biocentric/DeepVariantNF\n", + "515 Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/NorwegianVeterinaryInstitute/nextflow_patterns/emit_example.nf': The call for 'doo_foo' coudn't be found, before its use in the operation 'doo_foo.out.foo_item', possibly at line 44. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "516 Workflow-Corpus-Open-License/vierstralab/nf-genotyping\n", + "517 Workflow-Corpus-Open-License/vierstralab/nf-index\n", + "518 Workflow-Corpus-Open-License/guigolab/FA-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/guigolab/FA-nf/main.nf': Not the same number of opening and closing parentheses '()' in the file.\n", + "519 Workflow-Corpus-Open-License/guigolab/selenoprofiles-nf\n", + "520 Workflow-Corpus-Open-License/guigolab/sqtlseeker2-nf\n", + "521 Workflow-Corpus-Open-License/guigolab/geneidx\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/guigolab/geneidx/main.nf': Something went wrong in an include, possibly at line 34. No such file: 'Workflow-Corpus-Open-License/guigolab/geneidx/${wk_folder}/GENEIDX.nf'.\n", + "522 Workflow-Corpus-Open-License/guigolab/ipsa-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/guigolab/ipsa-nf/ipsa.nf': 'ssjA06' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "523 Workflow-Corpus-Open-License/quinlan-lab/STRling-nf\n", + "524 Workflow-Corpus-Open-License/mtuong/nextflow-tychus\n", + "525 Workflow-Corpus-Open-License/UCL-BLIC/nf-ginkgo\n", + "526 Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline\n", + "[10] Error in the file 'Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/subworkflows/local/input_check.nf': Something went wrong in an include, possibly at line 5. No such file: 'Workflow-Corpus-Open-License/WangLab-ComputationalBiology/btc-scrna-pipeline/modules/local/samplesheet_check.nf'.\n", + "527 Workflow-Corpus-Open-License/connor-lab/qc_nextflow\n", + "528 Workflow-Corpus-Open-License/lconde-ucl/rnaseq_variant_calling\n", + "529 Workflow-Corpus-Open-License/lconde-ucl/wgsalign\n", + "530 Workflow-Corpus-Open-License/lconde-ucl/DGE\n", + "531 Workflow-Corpus-Open-License/lconde-ucl/runthis\n", + "532 Workflow-Corpus-Open-License/lconde-ucl/merge_fastq\n", + "533 Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-GFE\n", + "534 Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-OptiType\n", + "535 Workflow-Corpus-Open-License/FilipThorn/nf_mito-mania\n", + "536 Workflow-Corpus-Open-License/sheynkman-lab/Long-Read-Proteogenomics\n", + "537 Workflow-Corpus-Open-License/erikrikarddaniel/magmap\n", + "538 Workflow-Corpus-Open-License/erikrikarddaniel/pfitmap-nextflow\n", + "539 Workflow-Corpus-Open-License/genepi/nf-gwas\n", + "540 Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/Plant-Food-Research-Open/assembly_qc/subworkflows/local/tidk.nf': 'set { ch_list_of_a_posteriori_tidk_plots }' is neither a process, subworkflow or an operator. In the executor 'ch_explored_repeat_seq\n", " .join(\n", " ch_sorted_hap_file\n", " )\n", @@ -826,45 +815,45 @@ " | PLOT_A_POSTERIORI_REPEAT_SEQ\n", " | collect\n", " | set { ch_list_of_a_posteriori_tidk_plots }', possibly at line 18.\n", - "542 ../../../Workflow-Corpus-Open-License/photocyte/luciferase-PPX-predictor-nf\n", - "543 ../../../Workflow-Corpus-Open-License/luslab/nf-clip\n", - "544 ../../../Workflow-Corpus-Open-License/lskatz/Kessel-run\n", - "545 ../../../Workflow-Corpus-Open-License/nf-core/raredisease\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/raredisease/workflows/raredisease.nf': To much to unpack : The subworkflow 'PREPARE_REFERENCES' emits over one channel in a operation, possibly at line 164.\n", - "546 ../../../Workflow-Corpus-Open-License/nf-core/cutandrun\n", - "547 ../../../Workflow-Corpus-Open-License/nf-core/cageseq\n", - "548 ../../../Workflow-Corpus-Open-License/nf-core/hlatyping\n", - "549 ../../../Workflow-Corpus-Open-License/nf-core/genomeannotator\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/genomeannotator/workflows/genomeannotator.nf': The call for 'AUGUSTUS_TRAINING' coudn't be found, before its use in the operation 'ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder', possibly at line 293. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "550 ../../../Workflow-Corpus-Open-License/nf-core/circrna\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/circrna/workflows/circrna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 115.\n", - "551 ../../../Workflow-Corpus-Open-License/nf-core/ampliseq\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/ampliseq/workflows/ampliseq.nf': To much to unpack : The subworkflow 'CUTADAPT_WORKFLOW' emits over one channel in a operation, possibly at line 323.\n", - "552 ../../../Workflow-Corpus-Open-License/nf-core/readsimulator\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/readsimulator/workflows/readsimulator/main.nf': The call for 'MERGE_FASTAS' coudn't be found, before its use in the operation 'ch_fasta = MERGE_FASTAS.out.fasta\n", + "541 Workflow-Corpus-Open-License/photocyte/luciferase-PPX-predictor-nf\n", + "542 Workflow-Corpus-Open-License/luslab/nf-clip\n", + "543 Workflow-Corpus-Open-License/lskatz/Kessel-run\n", + "544 Workflow-Corpus-Open-License/nf-core/raredisease\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/raredisease/workflows/raredisease.nf': To much to unpack : The subworkflow 'PREPARE_REFERENCES' emits over one channel in a operation, possibly at line 164.\n", + "545 Workflow-Corpus-Open-License/nf-core/cutandrun\n", + "546 Workflow-Corpus-Open-License/nf-core/cageseq\n", + "547 Workflow-Corpus-Open-License/nf-core/hlatyping\n", + "548 Workflow-Corpus-Open-License/nf-core/genomeannotator\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/genomeannotator/workflows/genomeannotator.nf': The call for 'AUGUSTUS_TRAINING' coudn't be found, before its use in the operation 'ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder', possibly at line 293. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "549 Workflow-Corpus-Open-License/nf-core/circrna\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/circrna/workflows/circrna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 115.\n", + "550 Workflow-Corpus-Open-License/nf-core/ampliseq\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/ampliseq/workflows/ampliseq.nf': To much to unpack : The subworkflow 'CUTADAPT_WORKFLOW' emits over one channel in a operation, possibly at line 323.\n", + "551 Workflow-Corpus-Open-License/nf-core/readsimulator\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/readsimulator/workflows/readsimulator/main.nf': The call for 'MERGE_FASTAS' coudn't be found, before its use in the operation 'ch_fasta = MERGE_FASTAS.out.fasta\n", " .map {\n", " meta, fasta ->\n", " return fasta\n", " }', possibly at line 109. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "553 ../../../Workflow-Corpus-Open-License/nf-core/chipseq\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/chipseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 177. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "554 ../../../Workflow-Corpus-Open-License/nf-core/crisprseq\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/crisprseq/workflows/crisprseq_targeted.nf': Tried to access the emit 'PREPROCESSING_SUMMARY.out.versions' but the Process 'PREPROCESSING_SUMMARY' has not been called in the subworkflow 'CRISPRSEQ_TARGETED'.\n", - "555 ../../../Workflow-Corpus-Open-License/nf-core/rnafusion\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnafusion/workflows/rnafusion.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 126.\n", - "556 ../../../Workflow-Corpus-Open-License/nf-core/hic\n", - "557 ../../../Workflow-Corpus-Open-License/nf-core/createpanelrefs\n", - "558 ../../../Workflow-Corpus-Open-License/nf-core/diaproteomics\n", - "559 ../../../Workflow-Corpus-Open-License/nf-core/mag\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/mag/subworkflows/local/binning.nf': Not the same number of parameters given as input for the subworklfow 'FASTA_BINNING_CONCOCT' in the call, possibly at line 97.\n", - "560 ../../../Workflow-Corpus-Open-License/nf-core/nanostring\n", - "561 ../../../Workflow-Corpus-Open-License/nf-core/detaxizer\n", - "562 ../../../Workflow-Corpus-Open-License/nf-core/variantcatalogue\n", - "563 ../../../Workflow-Corpus-Open-License/nf-core/funcscan\n", - "564 ../../../Workflow-Corpus-Open-License/nf-core/mhcquant\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/mhcquant/modules/local/samplesheet_check.nf': Multiple 'when:' were found in the process 'SAMPLESHEET_CHECK'.\n", - "565 ../../../Workflow-Corpus-Open-License/nf-core/airrflow\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/airrflow/subworkflows/local/assembled_input_check.nf': 'fa]$/\n", + "552 Workflow-Corpus-Open-License/nf-core/chipseq\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/chipseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 177. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "553 Workflow-Corpus-Open-License/nf-core/crisprseq\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/crisprseq/workflows/crisprseq_targeted.nf': Tried to access the emit 'PREPROCESSING_SUMMARY.out.versions' but the Process 'PREPROCESSING_SUMMARY' has not been called in the subworkflow 'CRISPRSEQ_TARGETED'.\n", + "554 Workflow-Corpus-Open-License/nf-core/rnafusion\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnafusion/workflows/rnafusion.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 126.\n", + "555 Workflow-Corpus-Open-License/nf-core/hic\n", + "556 Workflow-Corpus-Open-License/nf-core/createpanelrefs\n", + "557 Workflow-Corpus-Open-License/nf-core/diaproteomics\n", + "558 Workflow-Corpus-Open-License/nf-core/mag\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/nf-core/mag/subworkflows/local/binning.nf': Not the same number of parameters given as input for the subworklfow 'FASTA_BINNING_CONCOCT' in the call, possibly at line 97.\n", + "559 Workflow-Corpus-Open-License/nf-core/nanostring\n", + "560 Workflow-Corpus-Open-License/nf-core/detaxizer\n", + "561 Workflow-Corpus-Open-License/nf-core/variantcatalogue\n", + "562 Workflow-Corpus-Open-License/nf-core/funcscan\n", + "563 Workflow-Corpus-Open-License/nf-core/mhcquant\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/nf-core/mhcquant/modules/local/samplesheet_check.nf': Multiple 'when:' were found in the process 'SAMPLESHEET_CHECK'.\n", + "564 Workflow-Corpus-Open-License/nf-core/airrflow\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/nf-core/airrflow/subworkflows/local/assembled_input_check.nf': 'fa]$/\n", " tsv: it[0].filename =~ /tsv$/\n", " }\n", " .set{ ch_metadata }' is neither a process, subworkflow or an operator. In the executor 'ch_validated_input\n", @@ -875,160 +864,160 @@ " tsv: it[0].filename =~ /tsv$/\n", " }\n", " .set{ ch_metadata }', possibly at line 21.\n", - "566 ../../../Workflow-Corpus-Open-License/nf-core/pangenome\n", - "567 ../../../Workflow-Corpus-Open-License/nf-core/rnasplice\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnasplice/workflows/rnasplice.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 161.\n", - "568 ../../../Workflow-Corpus-Open-License/nf-core/bacass\n", - "569 ../../../Workflow-Corpus-Open-License/nf-core/demultiplex\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/demultiplex/workflows/demultiplex.nf': Tried to access the emit 'UNTAR.out.versions' but the Process 'UNTAR' has not been called in the subworkflow 'DEMULTIPLEX'.\n", - "570 ../../../Workflow-Corpus-Open-License/nf-core/exoseq\n", - "571 ../../../Workflow-Corpus-Open-License/nf-core/differentialabundance\n", - "572 ../../../Workflow-Corpus-Open-License/nf-core/smrnaseq\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/smrnaseq/workflows/smrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 104.\n", - "573 ../../../Workflow-Corpus-Open-License/nf-core/dualrnaseq\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/dualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "574 ../../../Workflow-Corpus-Open-License/nf-core/nascent\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/nascent/subworkflows/local/prepare_genome.nf': The call for 'UNTAR_DRAGMAP_INDEX' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)', possibly at line 122. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "575 ../../../Workflow-Corpus-Open-License/nf-core/marsseq\n", - "576 ../../../Workflow-Corpus-Open-License/nf-core/kmermaid\n", - "577 ../../../Workflow-Corpus-Open-License/nf-core/configs\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/configs/configtest.nf': No 'main' workflow was found.\n", - "578 ../../../Workflow-Corpus-Open-License/nf-core/spatialtranscriptomics\n", - "579 ../../../Workflow-Corpus-Open-License/nf-core/modules\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/modules/main.nf': No 'main' workflow was found.\n", - "580 ../../../Workflow-Corpus-Open-License/nf-core/eager\n", - "581 ../../../Workflow-Corpus-Open-License/nf-core/ssds\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/ssds/subworkflows/local/sort_and_index_bam.nf': The call for 'SAMTOOLS_SORTSAM' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SAMTOOLS_SORTSAM.out.versions.first())', possibly at line 17. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "582 ../../../Workflow-Corpus-Open-License/nf-core/rnaseq\n", - "583 ../../../Workflow-Corpus-Open-License/nf-core/phageannotator\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/phageannotator/workflows/phageannotator/main.nf': To much to unpack : The subworkflow 'FASTQ_VIRUS_ENRICHMENT_VIROMEQC' emits over one channel in a operation, possibly at line 78.\n", - "584 ../../../Workflow-Corpus-Open-License/nf-core/omicsgenetraitassociation\n", - "585 ../../../Workflow-Corpus-Open-License/nf-core/metaboigniter\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/metaboigniter/subworkflows/local/mergems1ms2.nf': 'OPENMS_FILEMERGER' is neither a process, subworkflow or an operator. In the executor 'mzml_files.filter{meta,file->meta.level != \"MS2\"}.combine(OPENMS_FILEFILTERMS2.out.mzml.map{it[1]}).groupTuple(by:[0,1]) | OPENMS_FILEMERGER', possibly at line 19.\n", - "586 ../../../Workflow-Corpus-Open-License/nf-core/epitopeprediction\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/epitopeprediction/workflows/epitopeprediction.nf': The call for 'SHOW_SUPPORTED_MODELS' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SHOW_SUPPORTED_MODELS.out.versions.ifEmpty(null))', possibly at line 180. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "587 ../../../Workflow-Corpus-Open-License/nf-core/vipr\n", - "588 ../../../Workflow-Corpus-Open-License/nf-core/methylseq\n", - "589 ../../../Workflow-Corpus-Open-License/nf-core/viralintegration\n", - "590 ../../../Workflow-Corpus-Open-License/nf-core/genomeassembler\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/genomeassembler/subworkflows/local/evaluate_gene_space.nf': Not the same number of parameters given as input for the process 'BUSCO', possibly at line 10.\n", - "591 ../../../Workflow-Corpus-Open-License/nf-core/circdna\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/circdna/workflows/circdna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 190.\n", - "592 ../../../Workflow-Corpus-Open-License/nf-core/fetchngs\n", - "[2] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/fetchngs/main.nf': Not the same number of parameters given as input for the subworklfow 'SYNAPSE' in the call, possibly at line 46.\n", - "593 ../../../Workflow-Corpus-Open-License/nf-core/multiplesequencealign\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/multiplesequencealign/modules/local/prepare_shiny.nf': Multiple 'when:' were found in the process 'PREPARE_SHINY'.\n", - "594 ../../../Workflow-Corpus-Open-License/nf-core/isoseq\n", - "595 ../../../Workflow-Corpus-Open-License/nf-core/pathogensurveillance\n", - "596 ../../../Workflow-Corpus-Open-License/nf-core/phyloplace\n", - "597 ../../../Workflow-Corpus-Open-License/nf-core/taxprofiler\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/taxprofiler/subworkflows/local/shortread_preprocessing.nf': To much to unpack : The subworkflow 'SHORTREAD_FASTP' emits over one channel in a operation, possibly at line 21.\n", - "598 ../../../Workflow-Corpus-Open-License/nf-core/metatdenovo\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/metatdenovo/workflows/metatdenovo.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 146.\n", - "599 ../../../Workflow-Corpus-Open-License/nf-core/viralrecon\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/viralrecon/workflows/illumina.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 163.\n", - "600 ../../../Workflow-Corpus-Open-License/nf-core/scrnaseq\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/scrnaseq/workflows/scrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 121.\n", - "601 ../../../Workflow-Corpus-Open-License/nf-core/fastquorum\n", - "602 ../../../Workflow-Corpus-Open-License/nf-core/rnadnavar\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnadnavar/subworkflows/local/prepare_genome/main.nf': The call for 'GUNZIP_GFF' coudn't be found, before its use in the operation 'ch_gff = GUNZIP_GFF.out.gunzip.map{ meta, gff -> [gff] }.collect()', possibly at line 98. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "603 ../../../Workflow-Corpus-Open-License/nf-core/bamtofastq\n", - "604 ../../../Workflow-Corpus-Open-License/nf-core/clipseq\n", - "605 ../../../Workflow-Corpus-Open-License/nf-core/neutronstar\n", - "606 ../../../Workflow-Corpus-Open-License/nf-core/rnavar\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/rnavar/workflows/rnavar.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 138.\n", - "607 ../../../Workflow-Corpus-Open-License/nf-core/createtaxdb\n", - "608 ../../../Workflow-Corpus-Open-License/nf-core/gwas\n", - "609 ../../../Workflow-Corpus-Open-License/nf-core/coproid\n", - "610 ../../../Workflow-Corpus-Open-License/nf-core/nanoseq\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/nanoseq/subworkflows/local/rna_modifications_xpore_m6anet.nf': Tried to access the emit 'NANOPOLISH_INDEX_EVENTALIGN.out.nanopolish_outputs' but the Process 'NANOPOLISH_INDEX_EVENTALIGN' has not been called in the subworkflow 'RNA_MODIFICATION_XPORE_M6ANET'.\n", - "611 ../../../Workflow-Corpus-Open-License/nf-core/sarek\n", - "612 ../../../Workflow-Corpus-Open-License/nf-core/radseq\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/radseq/workflows/radseq.nf': To much to unpack : The subworkflow 'CDHIT_RAINBOW' emits over one channel in a operation, possibly at line 97.\n", - "613 ../../../Workflow-Corpus-Open-License/nf-core/atacseq\n", - "[8] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/atacseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 199. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", - "614 ../../../Workflow-Corpus-Open-License/nf-core/proteinfold\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/proteinfold/workflows/alphafold2.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 81.\n", - "615 ../../../Workflow-Corpus-Open-License/nf-core/proteomicslfq\n", - "616 ../../../Workflow-Corpus-Open-License/nf-core/bactmap\n", - "617 ../../../Workflow-Corpus-Open-License/nf-core/mnaseseq\n", - "618 ../../../Workflow-Corpus-Open-License/nf-core/metapep\n", - "619 ../../../Workflow-Corpus-Open-License/nf-core/crisprvar\n", - "620 ../../../Workflow-Corpus-Open-License/nf-core/quantms\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/nf-core/quantms/workflows/quantms.nf': 'set {ch_db_for_decoy_creation_or_null}' is neither a process, subworkflow or an operator. In the executor 'CREATE_INPUT_CHANNEL.out.ch_meta_config_iso.mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq).first() \n", + "565 Workflow-Corpus-Open-License/nf-core/pangenome\n", + "566 Workflow-Corpus-Open-License/nf-core/rnasplice\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnasplice/workflows/rnasplice.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 161.\n", + "567 Workflow-Corpus-Open-License/nf-core/bacass\n", + "568 Workflow-Corpus-Open-License/nf-core/demultiplex\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/demultiplex/workflows/demultiplex.nf': Tried to access the emit 'UNTAR.out.versions' but the Process 'UNTAR' has not been called in the subworkflow 'DEMULTIPLEX'.\n", + "569 Workflow-Corpus-Open-License/nf-core/exoseq\n", + "570 Workflow-Corpus-Open-License/nf-core/differentialabundance\n", + "571 Workflow-Corpus-Open-License/nf-core/smrnaseq\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/smrnaseq/workflows/smrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 104.\n", + "572 Workflow-Corpus-Open-License/nf-core/dualrnaseq\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/nf-core/dualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "573 Workflow-Corpus-Open-License/nf-core/nascent\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/nascent/subworkflows/local/prepare_genome.nf': The call for 'UNTAR_DRAGMAP_INDEX' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)', possibly at line 122. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "574 Workflow-Corpus-Open-License/nf-core/marsseq\n", + "575 Workflow-Corpus-Open-License/nf-core/kmermaid\n", + "576 Workflow-Corpus-Open-License/nf-core/configs\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/nf-core/configs/configtest.nf': No 'main' workflow was found.\n", + "577 Workflow-Corpus-Open-License/nf-core/spatialtranscriptomics\n", + "578 Workflow-Corpus-Open-License/nf-core/modules\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/nf-core/modules/main.nf': No 'main' workflow was found.\n", + "579 Workflow-Corpus-Open-License/nf-core/eager\n", + "580 Workflow-Corpus-Open-License/nf-core/ssds\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/ssds/subworkflows/local/sort_and_index_bam.nf': The call for 'SAMTOOLS_SORTSAM' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SAMTOOLS_SORTSAM.out.versions.first())', possibly at line 17. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "581 Workflow-Corpus-Open-License/nf-core/rnaseq\n", + "582 Workflow-Corpus-Open-License/nf-core/phageannotator\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/phageannotator/workflows/phageannotator/main.nf': To much to unpack : The subworkflow 'FASTQ_VIRUS_ENRICHMENT_VIROMEQC' emits over one channel in a operation, possibly at line 78.\n", + "583 Workflow-Corpus-Open-License/nf-core/omicsgenetraitassociation\n", + "584 Workflow-Corpus-Open-License/nf-core/metaboigniter\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/nf-core/metaboigniter/subworkflows/local/mergems1ms2.nf': 'OPENMS_FILEMERGER' is neither a process, subworkflow or an operator. In the executor 'mzml_files.filter{meta,file->meta.level != \"MS2\"}.combine(OPENMS_FILEFILTERMS2.out.mzml.map{it[1]}).groupTuple(by:[0,1]) | OPENMS_FILEMERGER', possibly at line 19.\n", + "585 Workflow-Corpus-Open-License/nf-core/epitopeprediction\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/epitopeprediction/workflows/epitopeprediction.nf': The call for 'SHOW_SUPPORTED_MODELS' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(SHOW_SUPPORTED_MODELS.out.versions.ifEmpty(null))', possibly at line 180. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "586 Workflow-Corpus-Open-License/nf-core/vipr\n", + "587 Workflow-Corpus-Open-License/nf-core/methylseq\n", + "588 Workflow-Corpus-Open-License/nf-core/viralintegration\n", + "589 Workflow-Corpus-Open-License/nf-core/genomeassembler\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/nf-core/genomeassembler/subworkflows/local/evaluate_gene_space.nf': Not the same number of parameters given as input for the process 'BUSCO', possibly at line 10.\n", + "590 Workflow-Corpus-Open-License/nf-core/circdna\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/circdna/workflows/circdna.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 190.\n", + "591 Workflow-Corpus-Open-License/nf-core/fetchngs\n", + "[2] Error in the file 'Workflow-Corpus-Open-License/nf-core/fetchngs/main.nf': Not the same number of parameters given as input for the subworklfow 'SYNAPSE' in the call, possibly at line 46.\n", + "592 Workflow-Corpus-Open-License/nf-core/multiplesequencealign\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/nf-core/multiplesequencealign/modules/local/prepare_shiny.nf': Multiple 'when:' were found in the process 'PREPARE_SHINY'.\n", + "593 Workflow-Corpus-Open-License/nf-core/isoseq\n", + "594 Workflow-Corpus-Open-License/nf-core/pathogensurveillance\n", + "595 Workflow-Corpus-Open-License/nf-core/phyloplace\n", + "596 Workflow-Corpus-Open-License/nf-core/taxprofiler\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/taxprofiler/subworkflows/local/shortread_preprocessing.nf': To much to unpack : The subworkflow 'SHORTREAD_FASTP' emits over one channel in a operation, possibly at line 21.\n", + "597 Workflow-Corpus-Open-License/nf-core/metatdenovo\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/metatdenovo/workflows/metatdenovo.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 146.\n", + "598 Workflow-Corpus-Open-License/nf-core/viralrecon\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/viralrecon/workflows/illumina.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 163.\n", + "599 Workflow-Corpus-Open-License/nf-core/scrnaseq\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/scrnaseq/workflows/scrnaseq.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 121.\n", + "600 Workflow-Corpus-Open-License/nf-core/fastquorum\n", + "601 Workflow-Corpus-Open-License/nf-core/rnadnavar\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnadnavar/subworkflows/local/prepare_genome/main.nf': The call for 'GUNZIP_GFF' coudn't be found, before its use in the operation 'ch_gff = GUNZIP_GFF.out.gunzip.map{ meta, gff -> [gff] }.collect()', possibly at line 98. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "602 Workflow-Corpus-Open-License/nf-core/bamtofastq\n", + "603 Workflow-Corpus-Open-License/nf-core/clipseq\n", + "604 Workflow-Corpus-Open-License/nf-core/neutronstar\n", + "605 Workflow-Corpus-Open-License/nf-core/rnavar\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/rnavar/workflows/rnavar.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 138.\n", + "606 Workflow-Corpus-Open-License/nf-core/createtaxdb\n", + "607 Workflow-Corpus-Open-License/nf-core/gwas\n", + "608 Workflow-Corpus-Open-License/nf-core/coproid\n", + "609 Workflow-Corpus-Open-License/nf-core/nanoseq\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/nanoseq/subworkflows/local/rna_modifications_xpore_m6anet.nf': Tried to access the emit 'NANOPOLISH_INDEX_EVENTALIGN.out.nanopolish_outputs' but the Process 'NANOPOLISH_INDEX_EVENTALIGN' has not been called in the subworkflow 'RNA_MODIFICATION_XPORE_M6ANET'.\n", + "610 Workflow-Corpus-Open-License/nf-core/sarek\n", + "611 Workflow-Corpus-Open-License/nf-core/radseq\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/radseq/workflows/radseq.nf': To much to unpack : The subworkflow 'CDHIT_RAINBOW' emits over one channel in a operation, possibly at line 97.\n", + "612 Workflow-Corpus-Open-License/nf-core/atacseq\n", + "[8] Error in the file 'Workflow-Corpus-Open-License/nf-core/atacseq/subworkflows/local/prepare_genome.nf': The call for 'UNTAR' coudn't be found, before its use in the operation 'ch_versions = ch_versions.mix(UNTAR.out.versions)', possibly at line 199. Either because the call wasn't made before the operation or that the element it is calling doesn't exist.\n", + "613 Workflow-Corpus-Open-License/nf-core/proteinfold\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/nf-core/proteinfold/workflows/alphafold2.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 81.\n", + "614 Workflow-Corpus-Open-License/nf-core/proteomicslfq\n", + "615 Workflow-Corpus-Open-License/nf-core/bactmap\n", + "616 Workflow-Corpus-Open-License/nf-core/mnaseseq\n", + "617 Workflow-Corpus-Open-License/nf-core/metapep\n", + "618 Workflow-Corpus-Open-License/nf-core/crisprvar\n", + "619 Workflow-Corpus-Open-License/nf-core/quantms\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/nf-core/quantms/workflows/quantms.nf': 'set {ch_db_for_decoy_creation_or_null}' is neither a process, subworkflow or an operator. In the executor 'CREATE_INPUT_CHANNEL.out.ch_meta_config_iso.mix(CREATE_INPUT_CHANNEL.out.ch_meta_config_lfq).first() \n", " | combine( ch_db_for_decoy_creation ) \n", " | map { it[-1] } \n", " | set {ch_db_for_decoy_creation_or_null}', possibly at line 135.\n", - "621 ../../../Workflow-Corpus-Open-License/nf-core/imcyto\n", - "622 ../../../Workflow-Corpus-Open-License/andrecossa5/mito_preprocessing\n", - "623 ../../../Workflow-Corpus-Open-License/lisemangiante/test_nextflow\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/lisemangiante/test_nextflow/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file.\n", - "624 ../../../Workflow-Corpus-Open-License/dakoner/nextflow-example\n", - "625 ../../../Workflow-Corpus-Open-License/lifebit-ai/DeepVariant\n", - "626 ../../../Workflow-Corpus-Open-License/lifebit-ai/roary\n", - "627 ../../../Workflow-Corpus-Open-License/lifebit-ai/Plant-RNASeq\n", - "628 ../../../Workflow-Corpus-Open-License/lifebit-ai/onemetagenome\n", - "629 ../../../Workflow-Corpus-Open-License/jb-adams/variable-length-inputs-nf\n", - "630 ../../../Workflow-Corpus-Open-License/JingQiChong/nf_CRACpipeline\n", - "631 ../../../Workflow-Corpus-Open-License/juneb4869/new_meripseqpipe\n", - "632 ../../../Workflow-Corpus-Open-License/rmhubley/pseudo-it-nextflow\n", - "633 ../../../Workflow-Corpus-Open-License/louperelo/longmetarg\n", - "634 ../../../Workflow-Corpus-Open-License/j3551ca/BEAST-FLOW\n", - "635 ../../../Workflow-Corpus-Open-License/matsengrp/phip-flow\n", - "[14] Error in the file '../../../Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf': In the executor 'ds | to_csv | run_edgeR | run_BEER | (append_assay_csvs_to_xarray & publish_rds)', '(append_assay_csvs_to_xarray & publish_rds)' is neither a process, subworkflow or an operator (in the file '../../../Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf')\n", - "636 ../../../Workflow-Corpus-Open-License/raonyguimaraes/nextflow-hello\n", - "637 ../../../Workflow-Corpus-Open-License/MazdaX/nf-cage\n", - "638 ../../../Workflow-Corpus-Open-License/qbic-pipelines/rnadeseq\n", - "639 ../../../Workflow-Corpus-Open-License/qbic-pipelines/cellranger\n", - "640 ../../../Workflow-Corpus-Open-License/CollinsLabBioComp/nextflow-sc_dge\n", - "641 ../../../Workflow-Corpus-Open-License/dholab/nf-iWES\n", - "642 ../../../Workflow-Corpus-Open-License/avantonder/bovisanalyzer\n", - "643 ../../../Workflow-Corpus-Open-License/bigbio/pgdb\n", - "644 ../../../Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf/modules.nf': No 'main' workflow was found.\n", - "645 ../../../Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem\n", - "[20] Error in the file '../../../Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem/workflows/resequencing-mem.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 67.\n", - "646 ../../../Workflow-Corpus-Open-License/cnr-ibba/nf-neestimator\n", - "647 ../../../Workflow-Corpus-Open-License/alam1988/Nextflow\n", - "[12] Error in the file '../../../Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf': An include ('include { SRA_DOWNLOAD } from './sra_download'') was found in the main in the file '../../../Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf'. FlowInsight does not support this -> see specification list.\n", - "648 ../../../Workflow-Corpus-Open-License/OLC-Bioinformatics/BaitCapture\n", - "649 ../../../Workflow-Corpus-Open-License/nvnieuwk/nf-samplesheet-conversion\n", - "650 ../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf\n", - "[22] Error in the file '../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf/hybpiper.nf': Multiple 'take:' were found in the subworkflow 'fix_targetfile_main'.\n", - "651 ../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/paragone-nf\n", - "652 ../../../Workflow-Corpus-Open-License/VEuPathDB/marker-gene-analysis-16s-DADA2-nextflow\n", - "653 ../../../Workflow-Corpus-Open-License/VEuPathDB/psipred-nextflow\n", - "654 ../../../Workflow-Corpus-Open-License/VEuPathDB/dnaseq-nextflow\n", - "655 ../../../Workflow-Corpus-Open-License/VEuPathDB/mitoprot-nextflow\n", - "656 ../../../Workflow-Corpus-Open-License/VEuPathDB/gpi-anchor-prediction-nextflow\n", - "657 ../../../Workflow-Corpus-Open-License/VEuPathDB/hmmer-nextflow\n", - "658 ../../../Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB/main.nf': No 'main' workflow was found.\n", - "659 ../../../Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow\n", - "[6] Error in the file '../../../Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow/modules/bowtieMapping.nf': One channel was expected in the emit 'makeIndex.out'. Even though multiple emits are defined for the workflow 'makeIndex'\n", - "660 ../../../Workflow-Corpus-Open-License/PMCC-BioinformaticsCore/dinoflow\n", - "661 ../../../Workflow-Corpus-Open-License/Papatheodorou-Group/BENGAL\n", - "662 ../../../Workflow-Corpus-Open-License/OligoGeneticDiseases/oligo-nf\n", - "663 ../../../Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf/main.nf': No 'main' workflow was found.\n", - "664 ../../../Workflow-Corpus-Open-License/Arcadia-Science/metagenomics\n", - "665 ../../../Workflow-Corpus-Open-License/Arcadia-Science/seqqc\n", - "666 ../../../Workflow-Corpus-Open-License/ifremer-bioinformatics/samba\n", - "667 ../../../Workflow-Corpus-Open-License/dalmolingroup/bulkrna\n", - "668 ../../../Workflow-Corpus-Open-License/abyssum/NeoFuse2\n", - "669 ../../../Workflow-Corpus-Open-License/dhslab/nf-core-wgsnano\n", - "670 ../../../Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "671 ../../../Workflow-Corpus-Open-License/George-Marchment/hackathon\n", - "672 ../../../Workflow-Corpus-Open-License/msk-mind/clam-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/msk-mind/clam-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "673 ../../../Workflow-Corpus-Open-License/msk-mind/oncofusion-nf\n", - "[4] Error in the file '../../../Workflow-Corpus-Open-License/msk-mind/oncofusion-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", - "674 ../../../Workflow-Corpus-Open-License/daupt/hello-nextflow\n", - "675 ../../../Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline\n", - "[16] Error in the file '../../../Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline/main.nf': No 'main' workflow was found.\n", - "676 ../../../Workflow-Corpus-Open-License/crickbabs/BABS-MNASeqPE\n", - "677 ../../../Workflow-Corpus-Open-License/crickbabs/BABS-ATACSeqPE\n" + "620 Workflow-Corpus-Open-License/nf-core/imcyto\n", + "621 Workflow-Corpus-Open-License/andrecossa5/mito_preprocessing\n", + "622 Workflow-Corpus-Open-License/lisemangiante/test_nextflow\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/lisemangiante/test_nextflow/plot_coverage.nf': 'coverage' is trying to be created as a channel, possibly at line 3. It already exists as a process or a subworkflow in the nextflow file.\n", + "623 Workflow-Corpus-Open-License/dakoner/nextflow-example\n", + "624 Workflow-Corpus-Open-License/lifebit-ai/DeepVariant\n", + "625 Workflow-Corpus-Open-License/lifebit-ai/roary\n", + "626 Workflow-Corpus-Open-License/lifebit-ai/Plant-RNASeq\n", + "627 Workflow-Corpus-Open-License/lifebit-ai/onemetagenome\n", + "628 Workflow-Corpus-Open-License/jb-adams/variable-length-inputs-nf\n", + "629 Workflow-Corpus-Open-License/JingQiChong/nf_CRACpipeline\n", + "630 Workflow-Corpus-Open-License/juneb4869/new_meripseqpipe\n", + "631 Workflow-Corpus-Open-License/rmhubley/pseudo-it-nextflow\n", + "632 Workflow-Corpus-Open-License/louperelo/longmetarg\n", + "633 Workflow-Corpus-Open-License/j3551ca/BEAST-FLOW\n", + "634 Workflow-Corpus-Open-License/matsengrp/phip-flow\n", + "[14] Error in the file 'Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf': In the executor 'ds | to_csv | run_edgeR | run_BEER | (append_assay_csvs_to_xarray & publish_rds)', '(append_assay_csvs_to_xarray & publish_rds)' is neither a process, subworkflow or an operator (in the file 'Workflow-Corpus-Open-License/matsengrp/phip-flow/workflows/edgeR_BEER.nf')\n", + "635 Workflow-Corpus-Open-License/raonyguimaraes/nextflow-hello\n", + "636 Workflow-Corpus-Open-License/MazdaX/nf-cage\n", + "637 Workflow-Corpus-Open-License/qbic-pipelines/rnadeseq\n", + "638 Workflow-Corpus-Open-License/qbic-pipelines/cellranger\n", + "639 Workflow-Corpus-Open-License/CollinsLabBioComp/nextflow-sc_dge\n", + "640 Workflow-Corpus-Open-License/dholab/nf-iWES\n", + "641 Workflow-Corpus-Open-License/avantonder/bovisanalyzer\n", + "642 Workflow-Corpus-Open-License/bigbio/pgdb\n", + "643 Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/Ensembl/ensembl-genes-nf/modules.nf': No 'main' workflow was found.\n", + "644 Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem\n", + "[20] Error in the file 'Workflow-Corpus-Open-License/cnr-ibba/nf-resequencing-mem/workflows/resequencing-mem.nf': To much to unpack : The subworkflow 'INPUT_CHECK' emits over one channel in a operation, possibly at line 67.\n", + "645 Workflow-Corpus-Open-License/cnr-ibba/nf-neestimator\n", + "646 Workflow-Corpus-Open-License/alam1988/Nextflow\n", + "[12] Error in the file 'Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf': An include ('include { SRA_DOWNLOAD } from './sra_download'') was found in the main in the file 'Workflow-Corpus-Open-License/alam1988/Nextflow/main.nf'. FlowInsight does not support this -> see specification list.\n", + "647 Workflow-Corpus-Open-License/OLC-Bioinformatics/BaitCapture\n", + "648 Workflow-Corpus-Open-License/nvnieuwk/nf-samplesheet-conversion\n", + "649 Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf\n", + "[22] Error in the file 'Workflow-Corpus-Open-License/chrisjackson-pellicle/hybpiper-nf/hybpiper.nf': Multiple 'take:' were found in the subworkflow 'fix_targetfile_main'.\n", + "650 Workflow-Corpus-Open-License/chrisjackson-pellicle/paragone-nf\n", + "651 Workflow-Corpus-Open-License/VEuPathDB/marker-gene-analysis-16s-DADA2-nextflow\n", + "652 Workflow-Corpus-Open-License/VEuPathDB/psipred-nextflow\n", + "653 Workflow-Corpus-Open-License/VEuPathDB/dnaseq-nextflow\n", + "654 Workflow-Corpus-Open-License/VEuPathDB/mitoprot-nextflow\n", + "655 Workflow-Corpus-Open-License/VEuPathDB/gpi-anchor-prediction-nextflow\n", + "656 Workflow-Corpus-Open-License/VEuPathDB/hmmer-nextflow\n", + "657 Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/VEuPathDB/MicrobiomeDB/main.nf': No 'main' workflow was found.\n", + "658 Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow\n", + "[6] Error in the file 'Workflow-Corpus-Open-License/VEuPathDB/bowtie-mapping-nextflow/modules/bowtieMapping.nf': One channel was expected in the emit 'makeIndex.out'. Even though multiple emits are defined for the workflow 'makeIndex'\n", + "659 Workflow-Corpus-Open-License/PMCC-BioinformaticsCore/dinoflow\n", + "660 Workflow-Corpus-Open-License/Papatheodorou-Group/BENGAL\n", + "661 Workflow-Corpus-Open-License/OligoGeneticDiseases/oligo-nf\n", + "662 Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/PlantGGHLab/qiime2-nf/main.nf': No 'main' workflow was found.\n", + "663 Workflow-Corpus-Open-License/Arcadia-Science/metagenomics\n", + "664 Workflow-Corpus-Open-License/Arcadia-Science/seqqc\n", + "665 Workflow-Corpus-Open-License/ifremer-bioinformatics/samba\n", + "666 Workflow-Corpus-Open-License/dalmolingroup/bulkrna\n", + "667 Workflow-Corpus-Open-License/abyssum/NeoFuse2\n", + "668 Workflow-Corpus-Open-License/dhslab/nf-core-wgsnano\n", + "669 Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/bhagesh-codebeast/nextflowdualrnaseq/main.nf': 'salmon_index' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "670 Workflow-Corpus-Open-License/George-Marchment/hackathon\n", + "671 Workflow-Corpus-Open-License/msk-mind/clam-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/msk-mind/clam-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "672 Workflow-Corpus-Open-License/msk-mind/oncofusion-nf\n", + "[4] Error in the file 'Workflow-Corpus-Open-License/msk-mind/oncofusion-nf/main.nf': 'GET_SLIDES' is trying to be created as a channel. It already exists as a process or a subworkflow in the nextflow file.\n", + "673 Workflow-Corpus-Open-License/daupt/hello-nextflow\n", + "674 Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline\n", + "[16] Error in the file 'Workflow-Corpus-Open-License/sifrimlab/ST-nextflow-pipeline/main.nf': No 'main' workflow was found.\n", + "675 Workflow-Corpus-Open-License/crickbabs/BABS-MNASeqPE\n", + "676 Workflow-Corpus-Open-License/crickbabs/BABS-ATACSeqPE\n" ] } ], @@ -1076,7 +1065,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Analysed 75.37% (511) of the workflows succesfully. The others failed.\n" + "Analysed 75.48% (511) of the workflows succesfully. The others failed.\n" ] } ], @@ -1196,7 +1185,7 @@ "'3' : \"Unknown element used in a pipe operator.\",\n", "'5' : \"Ternary conditional operator used with a tuple.\",\n", "#'7' : \"Tuple with emit (ch1, ch2) = emit.out\",\n", - "'9' : \"Tuple associated with a call.\"#,#e.g. (ch1, ch2) = wf(),\n", + "'9' : \"Tuple associated with a call.\",#e.g. (ch1, ch2) = wf(),\n", "#'11' : \"Failed to extract the operation or call due to too complex syntax structure.\"\n", "}" ] @@ -1270,7 +1259,7 @@ " <tr>\n", " <th>16</th>\n", " <td>Syntax error in the code (e.g. not the same of...</td>\n", - " <td>35</td>\n", + " <td>34</td>\n", " </tr>\n", " <tr>\n", " <th>18</th>\n", @@ -1315,7 +1304,7 @@ "10 Tried to include a file which doesn't exist 14\n", "12 An include was present in a main or subworkflow 1\n", "14 In a pipe operator, the first thing called doe... 11\n", - "16 Syntax error in the code (e.g. not the same of... 35\n", + "16 Syntax error in the code (e.g. not the same of... 34\n", "18 Element (process or subworkflow) is expected t... 8\n", "20 A subworkflow either emits nothing or too many... 20\n", "22 A subworkflow or process was defined badly (e.... 10\n", @@ -1335,6 +1324,13 @@ "df.to_csv(\"different_errors_detected.csv\", sep='\\t', index=False)\n", "df" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": {