"'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",
"}"
]
},
...
...
%% Cell type:markdown id: tags:
# Analysis of a large dataset of workflows
%% Cell type:markdown id: tags:
> 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.
/usr/lib/python3/dist-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.1
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
%% Cell type:code id: tags:
``` python
sns.set(style='darkgrid',palette="Accent")
taille=(9,5)
```
%% Cell type:markdown id: tags:
## Parameters
%% Cell type:markdown id: tags:
These parameters allow the user to choose what elements of the analysis they want to be done.
%% Cell type:code id: tags:
``` python
#Bool to download workflow
download_files=False
#Path to folder containing workflows (where they will also be downloaded)
[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] 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] 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'.
[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.
[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.
[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.
[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.
[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.
[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.
[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
[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'.
[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.
[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'.
[16] Error in the file '../../../Workflow-Corpus-Open-License/abhi18av/nextflow_grid_search/stacked_ensemble_grid_search.nf': No 'main' workflow was found.
[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.
[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.
[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.
[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.
[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.
[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'.
[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()
[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.
[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 )
[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
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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)'.
[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.
[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.
[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.
[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'.
[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.
[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.
[16] Error in the file '../../../Workflow-Corpus-Open-License/Clinical-Genomics-Lund/nextflow-modules/bacteria-example.nf': No 'main' workflow was found.
[22] Error in the file '../../../Workflow-Corpus-Open-License/Euro-BioImaging/BatchConvert/modules/processes.nf': Multiple 'input:' were found in the process 'Convert_EachFileFromRoot2SeparateOMETIFF'.
[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.
[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.
[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'?
[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.
[22] Error in the file '../../../Workflow-Corpus-Open-License/fmalmeida/MpGAP/workflows/hybrid.nf': Multiple 'main:' were found in the subworkflow 'HYBRID'.
[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.
[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.
[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/${subwork_folder}/fastqc.nf'.
[10] Error in the file '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'.
[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.
[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'.
[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.
[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.
[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.
[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.
[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'.
[22] Error in the file '../../../Workflow-Corpus-Open-License/jtmccr1/beast_analysis/beast_analysis.nf': Multiple 'input:' were found in the process 'mcc'.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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.
[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.
[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'.
[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.
[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.
[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'.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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'.
[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
)
| SEARCH_A_POSTERIORI_REPEAT_SEQ
| PLOT_A_POSTERIORI_REPEAT_SEQ
| collect
| set { ch_list_of_a_posteriori_tidk_plots }', possibly at line 18.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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.
[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'.
[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.
[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'.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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.
[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.
[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.
[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.
[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.
[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'.
[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.
[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.
[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.
[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.
[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.
[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')
[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.
[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.
[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'.
[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'
[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.
[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.
[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.
_=group.plot(kind='pie',y='workflow',autopct=autopct_george(group),explode=explode,legend=False,title='Distribution of DSL versions between Nextflow workflows')
```
%% Output
%% Cell type:markdown id: tags:
## Anlysing Errors
%% Cell type:code id: tags:
``` python
pattern=r"\n *\[(\d+)\] "
withopen('failed_2_analyse.txt')asf:
errors=f.read()
```
%% Cell type:code id: tags:
``` python
dico_nb_errors={}
formatchinre.finditer(pattern,errors):
type_error=match.group(1)
try:
tmp=dico_nb_errors[type_error]
except:
dico_nb_errors[type_error]=0
dico_nb_errors[type_error]+=1
```
%% Cell type:code id: tags:
``` python
dico_type_errors={
'2':"Incorrect number of parameters given for a process or a subworkflow call",
'4':"Channel trying to be created with a name already given to an existing element",
'6':"Multiple channels are given by an emit even though only expecting one",
'8':"Tried to access an emit even though the element its emitting has not been called",
'10':"Tried to include a file which doesn't exist",
'12':"An include was present in a main or subworkflow",
'14':"In a pipe operator, the first thing called does not exist",
'16':"Syntax error in the code (e.g. not the same of parentheses)",
'18':"Element (process or subworkflow) is expected to be defined in a file but is not",
'20':"A subworkflow either emits nothing or too many values for use in an operation",
'22':"A subworkflow or process was defined badly (e.g. multiple input sections, multiple main sections...)",
#'1' : "presence of an import java or groovy (NOT USED RIGHT NOW)",
'3':"Unknown element used in a pipe operator.",
'5':"Ternary conditional operator used with a tuple.",
#'7' : "Tuple with emit (ch1, ch2) = emit.out",
'9':"Tuple associated with a call."#e.g. (ch1, ch2) = wf()
'9':"Tuple associated with a call."#,#e.g. (ch1, ch2) = wf(),
#'11' : "Failed to extract the operation or call due to too complex syntax structure."