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Commit 5960c59c authored by George Marchment's avatar George Marchment
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update

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%% 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.
%% Cell type:code id: tags:
``` python
import os
import json
import glob
import pandas as pd
import matplotlib as plt
import seaborn as sns
import re
current_path= os.getcwd()
os.chdir("github-crawler/")
from download_corpus import download
os.chdir(current_path)
os.chdir("bioflow-insight/")
from src.nextflow_file import Nextflow_File
from src.workflow import Workflow
from src.bioflowinsighterror import BioFlowInsightError
os.chdir(current_path)
```
%% Output
/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)
path_2_workflows = "../../../Workflow-Corpus-Open-License"
#Bool to run analysis ~6minutes on a 13th Gen Intel® Core™ i5-1335U × 12 (32gb of ram)
run_analysis_on_corpus = True
#Bool to analyse the results
analyse_results = True
```
%% Cell type:markdown id: tags:
## Creating the corpus
%% Cell type:code id: tags:
``` python
#Read crawler results
with open("./github-crawler/wf_crawl_nextflow.json") as json_file:
crawler = json.load(json_file)
_ = crawler.pop("last_date")
#Downloading the files
if(download_files):
download(path_2_workflows, crawler)
```
%% Cell type:markdown id: tags:
## Running the analysis on the corpus
%% Cell type:code id: tags:
``` python
workflows = glob.glob(f'{path_2_workflows}/*/*', recursive=False)
print(f"In total there are {len(workflows)} workflows.")
```
%% Output
In total there are 678 workflows.
%% Cell type:code id: tags:
``` python
DSL_tab = []
if(run_analysis_on_corpus):
index = 0
errors_string = ""
nb_errors = 0
for wf in workflows:
print(index, wf)
try:
nextflow_files = glob.glob(f'{wf}/**/*.nf', recursive=True)
try:
file = '/'.join(nextflow_files[0].split('/')[:-1])+"/main.nf"
with open(file, 'r') as f:
txt= f.read()
except:
file =nextflow_files[0]
w = Nextflow_File(file, duplicate=False, display_info=False)
w.initialise()
DSL_tab.append({"workflow":wf, "DSL":w.get_DSL()})
except BioFlowInsightError as e:
nb_errors+=1
errors_string+= f"- {index} {wf} \n {str(e)} \n\n"
text_file = open("failed_2_analyse.txt", "w")
n = text_file.write(errors_string)
text_file.close()
print(str(e))
index+=1
```
%% Output
0 ../../../Workflow-Corpus-Open-License/KevinMenden/hybrid-assembly
1 ../../../Workflow-Corpus-Open-License/ezorita/chip-nf
2 ../../../Workflow-Corpus-Open-License/GiantSpaceRobot/tsRNAsearch
3 ../../../Workflow-Corpus-Open-License/ctmrbio/BACTpipe
4 ../../../Workflow-Corpus-Open-License/wtsi-hgi/nf_cellbender
5 ../../../Workflow-Corpus-Open-License/grbot/run-fastqc
6 ../../../Workflow-Corpus-Open-License/grbot/nextflow-hack17-tutorial
7 ../../../Workflow-Corpus-Open-License/hunglin59638/plott
8 ../../../Workflow-Corpus-Open-License/codingene/nextflow-base
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'.
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'.
12 ../../../Workflow-Corpus-Open-License/Aveglia/vAMPirus
13 ../../../Workflow-Corpus-Open-License/telatin/cleanup
14 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/nf-methylpy
15 ../../../Workflow-Corpus-Open-License/Gregor-Mendel-Institute/kWIP-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.
17 ../../../Workflow-Corpus-Open-License/marcodelapierre/trinity-nf
18 ../../../Workflow-Corpus-Open-License/marcodelapierre/toy-gpu-nf
19 ../../../Workflow-Corpus-Open-License/marcodelapierre/nanopore-nf
20 ../../../Workflow-Corpus-Open-License/marcodelapierre/hello-nextflow
21 ../../../Workflow-Corpus-Open-License/marcodelapierre/illumina-nf
22 ../../../Workflow-Corpus-Open-License/maxemil/ALE-pipeline
23 ../../../Workflow-Corpus-Open-License/maxemil/Biodiversity-pipeline
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.
25 ../../../Workflow-Corpus-Open-License/brwnj/facets-nf
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.
27 ../../../Workflow-Corpus-Open-License/brwnj/idplot
28 ../../../Workflow-Corpus-Open-License/phc-health/nextflow-pangolin
29 ../../../Workflow-Corpus-Open-License/phipsonlab/NextClone
30 ../../../Workflow-Corpus-Open-License/SFGLab/ConsensuSV-nf-pipeline
31 ../../../Workflow-Corpus-Open-License/canceromics/MeRIPseqPipe
32 ../../../Workflow-Corpus-Open-License/AustralianBioCommons/Nextflow_DSL2_template
33 ../../../Workflow-Corpus-Open-License/AustralianBioCommons/hifi-assembly-workflow
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.
35 ../../../Workflow-Corpus-Open-License/stracquadaniolab/cubseq-nf
36 ../../../Workflow-Corpus-Open-License/stracquadaniolab/quick-rnaseq-nf
37 ../../../Workflow-Corpus-Open-License/APHA-CSU/hello-nextflow
38 ../../../Workflow-Corpus-Open-License/eipm/hello-mess-nf
39 ../../../Workflow-Corpus-Open-License/amchakra/tosca
40 ../../../Workflow-Corpus-Open-License/ksumngs/v-met
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.
43 ../../../Workflow-Corpus-Open-License/gerlichlab/scshic_pipeline
44 ../../../Workflow-Corpus-Open-License/pblaney/mgp1000
45 ../../../Workflow-Corpus-Open-License/Midnighter/nextflow-utility-services
46 ../../../Workflow-Corpus-Open-License/Midnighter/nf-slack
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'.
48 ../../../Workflow-Corpus-Open-License/BioImageTools/ome-zarr-image-analysis-nextflow
49 ../../../Workflow-Corpus-Open-License/BioImageTools/baysor-nextflow-module
50 ../../../Workflow-Corpus-Open-License/NajlaBioinfo/nextflow_tmpl
51 ../../../Workflow-Corpus-Open-License/didrikolofsson/rmappet
52 ../../../Workflow-Corpus-Open-License/lemaslab/rump
53 ../../../Workflow-Corpus-Open-License/replikation/docker_pipelines
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.
56 ../../../Workflow-Corpus-Open-License/wleepang/demo-genomics-workflow-nextflow
57 ../../../Workflow-Corpus-Open-License/sbilge/nextflow-clinvap
58 ../../../Workflow-Corpus-Open-License/NickSwainston/nextflow_tutorial
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.
60 ../../../Workflow-Corpus-Open-License/rdemko2332/downloadFromSra
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.
62 ../../../Workflow-Corpus-Open-License/adamd3/BactSeq
63 ../../../Workflow-Corpus-Open-License/yuukiiwa/CombiPIPE
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.
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.
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.
69 ../../../Workflow-Corpus-Open-License/EpiDiverse/snp
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.
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.
73 ../../../Workflow-Corpus-Open-License/TCLamnidis/contammix_pipeline
74 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-lofreq
75 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-bam-preprocessing
76 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-alignment
77 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-template
78 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-vcf-postprocessing
79 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-hla-hd
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'.
81 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/covigator-ngs-pipeline
82 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-mutect2
83 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-strelka2
84 ../../../Workflow-Corpus-Open-License/TRON-Bioinformatics/tronflow-haplotype-caller
85 ../../../Workflow-Corpus-Open-License/wishabc/nf-aligning
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.
87 ../../../Workflow-Corpus-Open-License/mribeirodantas/nf-whisper
88 ../../../Workflow-Corpus-Open-License/ewels/lightweight-template
89 ../../../Workflow-Corpus-Open-License/darcyabjones/snptree
90 ../../../Workflow-Corpus-Open-License/darcyabjones/mumflow
91 ../../../Workflow-Corpus-Open-License/bioinformaticsclouds/nextflow
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 )
| mix ( MINIMAP2_CLR.out.bam )
| 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.
94 ../../../Workflow-Corpus-Open-License/sanger-tol/treeval
95 ../../../Workflow-Corpus-Open-License/sanger-tol/curationpretext
96 ../../../Workflow-Corpus-Open-License/sanger-tol/gda
97 ../../../Workflow-Corpus-Open-License/sanger-tol/genomeassembly
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
| map { meta, bam -> [ meta + [ id: meta.id.split('_')[0..-2].join('_') ], bam ] }
| groupTuple ( by: [0] )
| set { ch_fastk }', possibly at line 62.
100 ../../../Workflow-Corpus-Open-License/edgano/TCoffee-NatureProtocol-nf
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.
102 ../../../Workflow-Corpus-Open-License/montilab/shine-nf
103 ../../../Workflow-Corpus-Open-License/montilab/pipeliner-2
104 ../../../Workflow-Corpus-Open-License/mmolari/genome-assembly
105 ../../../Workflow-Corpus-Open-License/dfornika/cpo-pipeline-nextflow
106 ../../../Workflow-Corpus-Open-License/dfornika/depth-analysis-nextflow
107 ../../../Workflow-Corpus-Open-License/rbpisupati/nf-haplocaller
108 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/lyz-nf
109 ../../../Workflow-Corpus-Open-License/NYU-Molecular-Pathology/demux-nf
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.
112 ../../../Workflow-Corpus-Open-License/tomsing1/nf-tutorial-blast
113 ../../../Workflow-Corpus-Open-License/idfarbanecha/benchmark-MeSS-CAMISIM
114 ../../../Workflow-Corpus-Open-License/DHQP/SNVPhyl_Nextflow
115 ../../../Workflow-Corpus-Open-License/nibscbioinformatics/nf-core-bagobugs
116 ../../../Workflow-Corpus-Open-License/dchebotarov/nextflow-variant-calling
117 ../../../Workflow-Corpus-Open-License/HPCBio/16S-rDNA-dada2-pipeline
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.
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.
122 ../../../Workflow-Corpus-Open-License/hnawar/nextflow-cloudrun
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.
124 ../../../Workflow-Corpus-Open-License/robsyme/markerdev
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.
126 ../../../Workflow-Corpus-Open-License/Boehringer-Ingelheim/flowml-pipeline
127 ../../../Workflow-Corpus-Open-License/dgarrimar/mvgwas-nf
128 ../../../Workflow-Corpus-Open-License/dgarrimar/gemma-nf
129 ../../../Workflow-Corpus-Open-License/axelwalter/diametalyzer
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.
131 ../../../Workflow-Corpus-Open-License/oist/LuscombeU_Nextflow_Pipeline_Template
132 ../../../Workflow-Corpus-Open-License/jhayer/baargin
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.
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)'.
136 ../../../Workflow-Corpus-Open-License/AndersenLab/nil-ril-nf
137 ../../../Workflow-Corpus-Open-License/AndersenLab/sv-nf
138 ../../../Workflow-Corpus-Open-License/AndersenLab/cegwas2-nf
139 ../../../Workflow-Corpus-Open-License/MaestSi/UMInator
140 ../../../Workflow-Corpus-Open-License/MaestSi/CharONT2
141 ../../../Workflow-Corpus-Open-License/MaestSi/nf-m6anet
142 ../../../Workflow-Corpus-Open-License/MaestSi/pycoMethFlow
143 ../../../Workflow-Corpus-Open-License/MaestSi/ONTrack2
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.
145 ../../../Workflow-Corpus-Open-License/lescailab/fenicsmpi
146 ../../../Workflow-Corpus-Open-License/Pooran-Dewari/SNP_array_nextflow
147 ../../../Workflow-Corpus-Open-License/Pooran-Dewari/Nextflow-pipeline-Extract-precise-location-of-gimme-maelstrom-TF-motifs
148 ../../../Workflow-Corpus-Open-License/lars20070/nextflow_lfq
149 ../../../Workflow-Corpus-Open-License/shaunchuah/cfdna_nextflow
150 ../../../Workflow-Corpus-Open-License/boulund/metagenome_pipeline
151 ../../../Workflow-Corpus-Open-License/PGScatalog/pgsc_calc
152 ../../../Workflow-Corpus-Open-License/ODiogoSilva/innuca-nf
153 ../../../Workflow-Corpus-Open-License/zamanianlab/Core_smRNAseq-nf
154 ../../../Workflow-Corpus-Open-License/sysbiomelab/meteor_pipeline
155 ../../../Workflow-Corpus-Open-License/lstevens17/nemAsm
156 ../../../Workflow-Corpus-Open-License/grst/minimal-nextflow-template
157 ../../../Workflow-Corpus-Open-License/grst/nextflow-notebook-pipeline
158 ../../../Workflow-Corpus-Open-License/grst/bd_rhapsody_velocyto
159 ../../../Workflow-Corpus-Open-License/grst/universal_analysis_pipeline
160 ../../../Workflow-Corpus-Open-License/friederhadlich/nextflow_ultraLowInput
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.
163 ../../../Workflow-Corpus-Open-License/MarieLataretu/nextflow-mwe
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'.
165 ../../../Workflow-Corpus-Open-License/SarahMaman/NextflowRNAseq
166 ../../../Workflow-Corpus-Open-License/angelovangel/nxf-kraken2
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.
169 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse19
170 ../../../Workflow-Corpus-Open-License/cbcrg/nf-phdcourse21
171 ../../../Workflow-Corpus-Open-License/cloud303-kloucks/nextflow-debugging
172 ../../../Workflow-Corpus-Open-License/noamteyssier/pipseq_nextflow
173 ../../../Workflow-Corpus-Open-License/noamteyssier/10x_rna_velocity_nextflow
174 ../../../Workflow-Corpus-Open-License/noamteyssier/sciseq_rna_velocity_nextflow
175 ../../../Workflow-Corpus-Open-License/uct-cbio/bacterial_variant_calling
176 ../../../Workflow-Corpus-Open-License/ameynert/nf-indelible
177 ../../../Workflow-Corpus-Open-License/OtimusOne/AFPAP
178 ../../../Workflow-Corpus-Open-License/nf-wrap/main
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.
180 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/nextflow-sra-cloud
181 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/pdx-nextflow
182 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/crf_nextflow_basics
183 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/ChIA-PIPE_nextflow
184 ../../../Workflow-Corpus-Open-License/TheJacksonLaboratory/mmrSVD
185 ../../../Workflow-Corpus-Open-License/evanfloden/stable-diffusion-nf
186 ../../../Workflow-Corpus-Open-License/evanfloden/nf-module-demo
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.
188 ../../../Workflow-Corpus-Open-License/HealthInnovationEast/cgpwgs-nf
189 ../../../Workflow-Corpus-Open-License/HealthInnovationEast/ExpansionHunter
190 ../../../Workflow-Corpus-Open-License/becavin-lab/nf-blast
191 ../../../Workflow-Corpus-Open-License/rsuchecki/nextflow-walkthrough
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.
193 ../../../Workflow-Corpus-Open-License/FischbachLab/nf-reads-profiler
194 ../../../Workflow-Corpus-Open-License/FischbachLab/nf-blast
195 ../../../Workflow-Corpus-Open-License/utia-gc/ngs
196 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-template
197 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-wf-megSAP
198 ../../../Workflow-Corpus-Open-License/qbicsoftware-archive/qbic-workflow-nf-rnaseq
199 ../../../Workflow-Corpus-Open-License/JacobLay/NextflowIntro
200 ../../../Workflow-Corpus-Open-License/OpenMSConsulting/NextflowLFQ
201 ../../../Workflow-Corpus-Open-License/vibbits/chipseq-nextflow
202 ../../../Workflow-Corpus-Open-License/OlgaChern/nextflow_gentrius_sim
203 ../../../Workflow-Corpus-Open-License/bkohrn/picard_demux_nextflow
204 ../../../Workflow-Corpus-Open-License/manuelesimi/hello-nextflow
205 ../../../Workflow-Corpus-Open-License/kkerns85/midas_nf_tower
206 ../../../Workflow-Corpus-Open-License/microgenlab/porefile
207 ../../../Workflow-Corpus-Open-License/open2c/distiller-nf
208 ../../../Workflow-Corpus-Open-License/MiGurke/nfmap
209 ../../../Workflow-Corpus-Open-License/MiGurke/nfvacal
210 ../../../Workflow-Corpus-Open-License/MiGurke/nfcongeneus
211 ../../../Workflow-Corpus-Open-License/tluquez/QUARS
212 ../../../Workflow-Corpus-Open-License/zhanyinx/metagenomics
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.
214 ../../../Workflow-Corpus-Open-License/aertslab/scenic-nf
215 ../../../Workflow-Corpus-Open-License/systems-genomics-lab/next-bgc
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'.
217 ../../../Workflow-Corpus-Open-License/bioShaun/om-nf-prepare
218 ../../../Workflow-Corpus-Open-License/bioShaun/xms-rnaseq-nf
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/lepsalex/nextflow-pcawg-bwa-mem-workflow
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.
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.
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.
224 ../../../Workflow-Corpus-Open-License/hoelzer/nf-hmmsearch
225 ../../../Workflow-Corpus-Open-License/hoelzer/dammit-nf
226 ../../../Workflow-Corpus-Open-License/hoelzer/virify
227 ../../../Workflow-Corpus-Open-License/peterk87/nf-flu
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.
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/jagedn/nextflow-groogle-sheet
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.
232 ../../../Workflow-Corpus-Open-License/openproblems-bio/openproblems-v2
233 ../../../Workflow-Corpus-Open-License/PRIDE-Archive/pride-molecule-indexer
234 ../../../Workflow-Corpus-Open-License/DaneVass/BARtab
235 ../../../Workflow-Corpus-Open-License/LeoniePohl/nextflow-diffexp-testpipeline
236 ../../../Workflow-Corpus-Open-License/stenglein-lab/viral_variant_caller
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.
238 ../../../Workflow-Corpus-Open-License/mattfemia/scrnaseq-pipeline
239 ../../../Workflow-Corpus-Open-License/MHH-RCUG/nf_wochenende
240 ../../../Workflow-Corpus-Open-License/DarianHole/test-nextflow
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'.
242 ../../../Workflow-Corpus-Open-License/fmalmeida/bacannot
243 ../../../Workflow-Corpus-Open-License/uel3/UnO_nf
244 ../../../Workflow-Corpus-Open-License/nttg8100/Simple-RNA-seq-Nextflow-with-Salmon
245 ../../../Workflow-Corpus-Open-License/fredjaya/msmc-nf
246 ../../../Workflow-Corpus-Open-License/pgonzale60/nxf_pipelines
247 ../../../Workflow-Corpus-Open-License/noepozzan/small-peptide-pipeline
248 ../../../Workflow-Corpus-Open-License/lukfor/pgs-calc-nf
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.
250 ../../../Workflow-Corpus-Open-License/biocorecrg/nf-cloud-gpu-test
251 ../../../Workflow-Corpus-Open-License/biocorecrg/MOP2
252 ../../../Workflow-Corpus-Open-License/biocorecrg/nextflow_detached_db_wrapper
253 ../../../Workflow-Corpus-Open-License/NCBI-Hackathons/ATACFlow
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.
255 ../../../Workflow-Corpus-Open-License/breichholf/smRNAseq
256 ../../../Workflow-Corpus-Open-License/nextflow-io/cwl2nxf
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.
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/${subwork_folder}/fastqc.nf'.
259 ../../../Workflow-Corpus-Open-License/nextflow-io/gccbosc18-training
260 ../../../Workflow-Corpus-Open-License/nextflow-io/socks
261 ../../../Workflow-Corpus-Open-License/JackCurragh/Nextflow-Template
262 ../../../Workflow-Corpus-Open-License/ZuberLab/mageck-nf
263 ../../../Workflow-Corpus-Open-License/ZuberLab/vbcf-nf
264 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-mageck-nf
265 ../../../Workflow-Corpus-Open-License/ZuberLab/guidemapper-nf
266 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-process-nf
267 ../../../Workflow-Corpus-Open-License/ZuberLab/crispr-nf
268 ../../../Workflow-Corpus-Open-License/ZuberLab/sra-nf
269 ../../../Workflow-Corpus-Open-License/oxfordfun/FunSnippy
270 ../../../Workflow-Corpus-Open-License/mmatthews06/nextflow-playground
271 ../../../Workflow-Corpus-Open-License/ricomnl/bioinformatics-pipeline-tutorial
272 ../../../Workflow-Corpus-Open-License/dolphinnext/rnaseq
273 ../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy
[10] Error in the file '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/main.nf': Something went wrong in an include, possibly at line 449. No such file: '../../../Workflow-Corpus-Open-License/LieberInstitute/SPEAQeasy/${workflow.projectDir}/modules/pull_annotation.nf'.
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.
275 ../../../Workflow-Corpus-Open-License/isugifNF/blast
276 ../../../Workflow-Corpus-Open-License/vmikk/BatchBlaster
277 ../../../Workflow-Corpus-Open-License/vmikk/PhyloNext
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.
279 ../../../Workflow-Corpus-Open-License/pcrxn/ProkkaFlow
280 ../../../Workflow-Corpus-Open-License/alneberg/trigger_error_nf
281 ../../../Workflow-Corpus-Open-License/opencobra/jeweler
282 ../../../Workflow-Corpus-Open-License/faithman/variant-nf
283 ../../../Workflow-Corpus-Open-License/digenoma-lab/nf-groot
284 ../../../Workflow-Corpus-Open-License/digenoma-lab/k-count-nf
285 ../../../Workflow-Corpus-Open-License/ATpoint/nf_findMotifs
286 ../../../Workflow-Corpus-Open-License/eQTL-Catalogue/colocalisation
287 ../../../Workflow-Corpus-Open-License/eQTL-Catalogue/susie-workflow
288 ../../../Workflow-Corpus-Open-License/veidenberg/tools-api-nextflow
289 ../../../Workflow-Corpus-Open-License/RibosomeCRCL/ribomethseq-nf
290 ../../../Workflow-Corpus-Open-License/anajung/CZI_addon
291 ../../../Workflow-Corpus-Open-License/cometsong/gbrs_nxf
292 ../../../Workflow-Corpus-Open-License/cometsong/ATAC_Seq_nxf
293 ../../../Workflow-Corpus-Open-License/jvierstra/nf-rnaseq
294 ../../../Workflow-Corpus-Open-License/RHReynolds/mkfastq
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'.
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.
297 ../../../Workflow-Corpus-Open-License/tiagofilipe12/pATLASflow
298 ../../../Workflow-Corpus-Open-License/usafsam/mad_river_wf
299 ../../../Workflow-Corpus-Open-License/sebgoti/spatial-pipeline
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.
301 ../../../Workflow-Corpus-Open-License/cedarwarman/pollen_cv_nextflow
302 ../../../Workflow-Corpus-Open-License/lehtiolab/nf-msconvert
303 ../../../Workflow-Corpus-Open-License/lehtiolab/ddamsproteomics
304 ../../../Workflow-Corpus-Open-License/stajichlab/nf-comparative-genomics
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/oalmelid/lift-over-nf
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.
308 ../../../Workflow-Corpus-Open-License/eastgenomics/mutect2_nextflow
309 ../../../Workflow-Corpus-Open-License/eastgenomics/VerifyBamID_nextflow
310 ../../../Workflow-Corpus-Open-License/BU-ISCIII/bacterial_assembly-nf
311 ../../../Workflow-Corpus-Open-License/BU-ISCIII/panelLowFreq-nf
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.
313 ../../../Workflow-Corpus-Open-License/AllenInstitute/deepinterpolation_nextflow
314 ../../../Workflow-Corpus-Open-License/sergpolly/random-nextflow-utils
315 ../../../Workflow-Corpus-Open-License/CIBERER-pipelines/mosaicism_nextflow
316 ../../../Workflow-Corpus-Open-License/EnriqueDoster/bioinformatic-nextflow-pipelines
317 ../../../Workflow-Corpus-Open-License/AlfredUg/QuasiFlow
318 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-model2data
319 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synstage
320 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-synindex
321 ../../../Workflow-Corpus-Open-License/Sage-Bionetworks-Workflows/nf-genie
322 ../../../Workflow-Corpus-Open-License/vntasis/stan-nf
323 ../../../Workflow-Corpus-Open-License/maxibor/kraken-nf
324 ../../../Workflow-Corpus-Open-License/maxibor/organdiet
325 ../../../Workflow-Corpus-Open-License/nkrumm/hello
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'.
327 ../../../Workflow-Corpus-Open-License/GunzIvan28/nextflow-rMAP-devt
328 ../../../Workflow-Corpus-Open-License/CCBR/CHAMPAGNE
329 ../../../Workflow-Corpus-Open-License/CCBR/CCBR_NextflowTemplate
330 ../../../Workflow-Corpus-Open-License/gleisonm/nextflow_bigscape
331 ../../../Workflow-Corpus-Open-License/aws-samples/aws-gatk-recipe-nextflow-pipeline
332 ../../../Workflow-Corpus-Open-License/thanhleviet/nextflow-ratt
333 ../../../Workflow-Corpus-Open-License/transXpress/transXpress-nextflow
334 ../../../Workflow-Corpus-Open-License/marc-jones/nextflow-example
335 ../../../Workflow-Corpus-Open-License/kenibrewer/shapeseq
336 ../../../Workflow-Corpus-Open-License/kenibrewer/simplenextflow
337 ../../../Workflow-Corpus-Open-License/gwright99/hello-nonmain
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'.
339 ../../../Workflow-Corpus-Open-License/crashGoBoom/nf-video
340 ../../../Workflow-Corpus-Open-License/Dowell-Lab/RNAseq-Flow
341 ../../../Workflow-Corpus-Open-License/Dowell-Lab/Bidirectional-Flow
342 ../../../Workflow-Corpus-Open-License/Dowell-Lab/Analysis-Flow
343 ../../../Workflow-Corpus-Open-License/Dowell-Lab/ChIP-Flow
344 ../../../Workflow-Corpus-Open-License/bguo068/snp_call_nf
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.
346 ../../../Workflow-Corpus-Open-License/salzman-lab/SpliZ
347 ../../../Workflow-Corpus-Open-License/KohlbacherLab/nextflow-clinvap
348 ../../../Workflow-Corpus-Open-License/ChrisgKent/flye-on-cluster
349 ../../../Workflow-Corpus-Open-License/RenneLab/CnR-flow
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.
351 ../../../Workflow-Corpus-Open-License/shenwei356/blast-nf
352 ../../../Workflow-Corpus-Open-License/ralsallaq/metaGx_nf
353 ../../../Workflow-Corpus-Open-License/ikmb-denbi/genome-annotation
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/sauriiiin/rnaseeker
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.
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.
358 ../../../Workflow-Corpus-Open-License/FloWuenne/nextflow_saige_dsl2
359 ../../../Workflow-Corpus-Open-License/FloWuenne/meta-METAL_nextflow_dsl2
360 ../../../Workflow-Corpus-Open-License/olgabot/nextflow-test-aws
361 ../../../Workflow-Corpus-Open-License/heuermh/minnebar15-workflow
362 ../../../Workflow-Corpus-Open-License/kviljoen/uct-srst2
363 ../../../Workflow-Corpus-Open-License/kviljoen/EMIRGE_nextflow
364 ../../../Workflow-Corpus-Open-License/tuzov/nf-cg-helloworld
365 ../../../Workflow-Corpus-Open-License/t-neumann/salmon-nf
366 ../../../Workflow-Corpus-Open-License/FredHutch/souper-star
367 ../../../Workflow-Corpus-Open-License/FredHutch/VMAA
368 ../../../Workflow-Corpus-Open-License/FredHutch/workflow-template-nextflow
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.
370 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_4
371 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1_print_hello_world
372 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_cookbook_1
373 ../../../Workflow-Corpus-Open-License/richelbilderbeek/nextflow_example_5
374 ../../../Workflow-Corpus-Open-License/danielecook/nextflow-tutorial
375 ../../../Workflow-Corpus-Open-License/rnajena/RNAswarm
376 ../../../Workflow-Corpus-Open-License/tdelhomme/vcf_ancestry-nf
377 ../../../Workflow-Corpus-Open-License/tdelhomme/SimulateLowCovSeq-nf
378 ../../../Workflow-Corpus-Open-License/tdelhomme/variantfiltering-nf
379 ../../../Workflow-Corpus-Open-License/tdelhomme/RegionalEnrichment-nf
380 ../../../Workflow-Corpus-Open-License/tdelhomme/SV-simulation-nf
381 ../../../Workflow-Corpus-Open-License/PavriLab/repliseq-nf
382 ../../../Workflow-Corpus-Open-License/PavriLab/geneIS-nf
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.
384 ../../../Workflow-Corpus-Open-License/gp201/Freyja_pathogen_workflow_alpha
385 ../../../Workflow-Corpus-Open-License/IARCbioinfo/LiftOver-nf
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.
387 ../../../Workflow-Corpus-Open-License/IARCbioinfo/TCGA_platypus-nf
388 ../../../Workflow-Corpus-Open-License/IARCbioinfo/CODEX-nf
389 ../../../Workflow-Corpus-Open-License/IARCbioinfo/purple-nf
390 ../../../Workflow-Corpus-Open-License/IARCbioinfo/table_annovar-nf
391 ../../../Workflow-Corpus-Open-License/IARCbioinfo/octopus-nf
392 ../../../Workflow-Corpus-Open-License/IARCbioinfo/damage-estimator-nf
393 ../../../Workflow-Corpus-Open-License/IARCbioinfo/NGSCheckMate-nf
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.
395 ../../../Workflow-Corpus-Open-License/IARCbioinfo/gatk4-DataPreProcessing-nf
396 ../../../Workflow-Corpus-Open-License/IARCbioinfo/template-nf
397 ../../../Workflow-Corpus-Open-License/IARCbioinfo/ampliconarchitect-nf
398 ../../../Workflow-Corpus-Open-License/IARCbioinfo/bamsurgeon-nf
399 ../../../Workflow-Corpus-Open-License/IARCbioinfo/BQSR-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'.
401 ../../../Workflow-Corpus-Open-License/jianhong/nextflowTutorial
402 ../../../Workflow-Corpus-Open-License/likelet/ExomePipe
403 ../../../Workflow-Corpus-Open-License/bentsherman/tesseract
404 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/dragonflye-nf
405 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/covflo
406 ../../../Workflow-Corpus-Open-License/BCCDC-PHL/fluflo
407 ../../../Workflow-Corpus-Open-License/bhargava-morampalli/cdnaseqont-nextflow
408 ../../../Workflow-Corpus-Open-License/pandora414/ssnp
409 ../../../Workflow-Corpus-Open-License/pandora414/lncRNA
410 ../../../Workflow-Corpus-Open-License/austinreidmanny/tvv-nf
411 ../../../Workflow-Corpus-Open-License/stevekm/nextflow-communicator
412 ../../../Workflow-Corpus-Open-License/stevekm/newfile-detector-nf
413 ../../../Workflow-Corpus-Open-License/keoughkath/GBGCnf
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.
415 ../../../Workflow-Corpus-Open-License/team113sanger/t113_irods_to_lustre
416 ../../../Workflow-Corpus-Open-License/BrianLohman/pdx-nf
417 ../../../Workflow-Corpus-Open-License/BrianLohman/ctseq-nf
418 ../../../Workflow-Corpus-Open-License/BrianLohman/RNAseq-variant-calling-nf
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.
420 ../../../Workflow-Corpus-Open-License/WarrenLab/longread-polish-nf
421 ../../../Workflow-Corpus-Open-License/WarrenLab/longread-svs-nf
422 ../../../Workflow-Corpus-Open-License/WarrenLab/shortread-polish-nf
423 ../../../Workflow-Corpus-Open-License/WarrenLab/purge-haplotigs-nf
424 ../../../Workflow-Corpus-Open-License/WarrenLab/minigraph-cactus-nf
425 ../../../Workflow-Corpus-Open-License/WarrenLab/cellranger-nf
426 ../../../Workflow-Corpus-Open-License/WarrenLab/hic-scaffolding-nf
427 ../../../Workflow-Corpus-Open-License/limrp/nextflow_metagenomics
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.
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.
430 ../../../Workflow-Corpus-Open-License/seqeralabs/nf-canary
431 ../../../Workflow-Corpus-Open-License/arontommi/RNAseq-VAX
432 ../../../Workflow-Corpus-Open-License/ObenaufLab/snv-calling-nf
433 ../../../Workflow-Corpus-Open-License/ObenaufLab/sv-calling-nf
434 ../../../Workflow-Corpus-Open-License/ObenaufLab/virus-detection-nf
435 ../../../Workflow-Corpus-Open-License/Streit-lab/enhancer_annotation_and_motif_analysis
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.
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'.
438 ../../../Workflow-Corpus-Open-License/PAIN-initiative/nextflow-scRNAseq
439 ../../../Workflow-Corpus-Open-License/Ratoncito/callingcards
440 ../../../Workflow-Corpus-Open-License/x-kiana/nextflow_pipeline
441 ../../../Workflow-Corpus-Open-License/cellgeni/nf-workshop
442 ../../../Workflow-Corpus-Open-License/cellgeni/rnaseq
443 ../../../Workflow-Corpus-Open-License/cellgeni/scmapIndex
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.
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.
446 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/fastqc-nf
447 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/bamQC-nf
448 ../../../Workflow-Corpus-Open-License/Sydney-Informatics-Hub/Germline-StructuralV-nf
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.
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'.
451 ../../../Workflow-Corpus-Open-License/mlf-core/nextflow-lcep
452 ../../../Workflow-Corpus-Open-License/wbazant/nextflow-hello-dsl2
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.
454 ../../../Workflow-Corpus-Open-License/samlhao/nf-core-abricate
455 ../../../Workflow-Corpus-Open-License/samlhao/hgtsimulation
456 ../../../Workflow-Corpus-Open-License/samlhao/nextflow-spid
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.
458 ../../../Workflow-Corpus-Open-License/robomics/generate_higlass_gene_track
459 ../../../Workflow-Corpus-Open-License/alexthiery/modify-gtf
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.
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.
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.
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.
464 ../../../Workflow-Corpus-Open-License/Mxrcon/Savio_alignments_nf
465 ../../../Workflow-Corpus-Open-License/csiro-crop-informatics/repset
466 ../../../Workflow-Corpus-Open-License/csiro-crop-informatics/nextflow-embl-abr-webinar
467 ../../../Workflow-Corpus-Open-License/mhebrard/TrimFlow
468 ../../../Workflow-Corpus-Open-License/jowkar/xenocell_nextflow
469 ../../../Workflow-Corpus-Open-License/tthyer/nextflow-scratch
470 ../../../Workflow-Corpus-Open-License/julesjacobsen/nextflow-test
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.
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.
473 ../../../Workflow-Corpus-Open-License/bts76-pitt/BCR_nextflow
474 ../../../Workflow-Corpus-Open-License/dnieuw/ENA_SARS_Cov2_nanopore
475 ../../../Workflow-Corpus-Open-License/nf-modules-hub/mykrobe
476 ../../../Workflow-Corpus-Open-License/nf-modules-hub/tb-profiler
477 ../../../Workflow-Corpus-Open-License/nf-modules-hub/mtbseq
478 ../../../Workflow-Corpus-Open-License/nf-modules-hub/gzip
479 ../../../Workflow-Corpus-Open-License/nf-modules-hub/snippy
480 ../../../Workflow-Corpus-Open-License/nf-modules-hub/trimmomatic
481 ../../../Workflow-Corpus-Open-License/nf-modules-hub/rd-analyzer
482 ../../../Workflow-Corpus-Open-License/nf-modules-hub/prokka
483 ../../../Workflow-Corpus-Open-License/nf-modules-hub/spotyping
484 ../../../Workflow-Corpus-Open-License/nf-modules-hub/kvarq
485 ../../../Workflow-Corpus-Open-License/nf-modules-hub/multiqc
486 ../../../Workflow-Corpus-Open-License/nf-modules-hub/nextflow_hub_process
487 ../../../Workflow-Corpus-Open-License/nf-modules-hub/quast
488 ../../../Workflow-Corpus-Open-License/nf-modules-hub/spades
489 ../../../Workflow-Corpus-Open-License/nf-modules-hub/rclone
490 ../../../Workflow-Corpus-Open-License/nf-modules-hub/fastqc
491 ../../../Workflow-Corpus-Open-License/mja/ukb-release-nf
492 ../../../Workflow-Corpus-Open-License/asereewit/rsv_ampseq
493 ../../../Workflow-Corpus-Open-License/scilus/dmriqc_flow
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/khigashi1987/CUTRUN_Nextflow
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/Nextstrain_Build
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.
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.
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.
501 ../../../Workflow-Corpus-Open-License/jallen73/teloSealer
502 ../../../Workflow-Corpus-Open-License/sidorov-si/nextflow-example-start
503 ../../../Workflow-Corpus-Open-License/gongyh/nf-core-scp
504 ../../../Workflow-Corpus-Open-License/gongyh/nf-core-scgs
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.
506 ../../../Workflow-Corpus-Open-License/ikmb/gwas-qc
507 ../../../Workflow-Corpus-Open-License/ikmb/gwas-assoc
508 ../../../Workflow-Corpus-Open-License/ikmb/finemapping
509 ../../../Workflow-Corpus-Open-License/ikmb/TOFU-MAaPO
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'.
511 ../../../Workflow-Corpus-Open-License/phue/GWAS-nf
512 ../../../Workflow-Corpus-Open-License/athbaltzis/paralogs-nf
513 ../../../Workflow-Corpus-Open-License/athbaltzis/diff-AS-nf
514 ../../../Workflow-Corpus-Open-License/apeltzer/IGCG-featureCounts
515 ../../../Workflow-Corpus-Open-License/Biocentric/DeepVariantNF
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.
517 ../../../Workflow-Corpus-Open-License/vierstralab/nf-genotyping
518 ../../../Workflow-Corpus-Open-License/vierstralab/nf-index
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.
520 ../../../Workflow-Corpus-Open-License/guigolab/selenoprofiles-nf
521 ../../../Workflow-Corpus-Open-License/guigolab/sqtlseeker2-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'.
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.
524 ../../../Workflow-Corpus-Open-License/quinlan-lab/STRling-nf
525 ../../../Workflow-Corpus-Open-License/mtuong/nextflow-tychus
526 ../../../Workflow-Corpus-Open-License/UCL-BLIC/nf-ginkgo
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'.
528 ../../../Workflow-Corpus-Open-License/connor-lab/qc_nextflow
529 ../../../Workflow-Corpus-Open-License/lconde-ucl/rnaseq_variant_calling
530 ../../../Workflow-Corpus-Open-License/lconde-ucl/wgsalign
531 ../../../Workflow-Corpus-Open-License/lconde-ucl/DGE
532 ../../../Workflow-Corpus-Open-License/lconde-ucl/runthis
533 ../../../Workflow-Corpus-Open-License/lconde-ucl/merge_fastq
534 ../../../Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-GFE
535 ../../../Workflow-Corpus-Open-License/nmdp-bioinformatics/flow-OptiType
536 ../../../Workflow-Corpus-Open-License/FilipThorn/nf_mito-mania
537 ../../../Workflow-Corpus-Open-License/sheynkman-lab/Long-Read-Proteogenomics
538 ../../../Workflow-Corpus-Open-License/erikrikarddaniel/magmap
539 ../../../Workflow-Corpus-Open-License/erikrikarddaniel/pfitmap-nextflow
540 ../../../Workflow-Corpus-Open-License/genepi/nf-gwas
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
.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.
542 ../../../Workflow-Corpus-Open-License/photocyte/luciferase-PPX-predictor-nf
543 ../../../Workflow-Corpus-Open-License/luslab/nf-clip
544 ../../../Workflow-Corpus-Open-License/lskatz/Kessel-run
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.
546 ../../../Workflow-Corpus-Open-License/nf-core/cutandrun
547 ../../../Workflow-Corpus-Open-License/nf-core/cageseq
548 ../../../Workflow-Corpus-Open-License/nf-core/hlatyping
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.
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.
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.
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
.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.
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'.
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.
556 ../../../Workflow-Corpus-Open-License/nf-core/hic
557 ../../../Workflow-Corpus-Open-License/nf-core/createpanelrefs
558 ../../../Workflow-Corpus-Open-License/nf-core/diaproteomics
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.
560 ../../../Workflow-Corpus-Open-License/nf-core/nanostring
561 ../../../Workflow-Corpus-Open-License/nf-core/detaxizer
562 ../../../Workflow-Corpus-Open-License/nf-core/variantcatalogue
563 ../../../Workflow-Corpus-Open-License/nf-core/funcscan
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'.
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]$/
tsv: it[0].filename =~ /tsv$/
}
.set{ ch_metadata }' is neither a process, subworkflow or an operator. In the executor 'ch_validated_input
.splitCsv(header: true, sep:'\t')
.map { get_meta(it) }
.branch { it ->
fasta: it[0].filename =~ /[fasta|fa]$/
tsv: it[0].filename =~ /tsv$/
}
.set{ ch_metadata }', possibly at line 21.
566 ../../../Workflow-Corpus-Open-License/nf-core/pangenome
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.
568 ../../../Workflow-Corpus-Open-License/nf-core/bacass
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'.
570 ../../../Workflow-Corpus-Open-License/nf-core/exoseq
571 ../../../Workflow-Corpus-Open-License/nf-core/differentialabundance
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.
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.
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.
575 ../../../Workflow-Corpus-Open-License/nf-core/marsseq
576 ../../../Workflow-Corpus-Open-License/nf-core/kmermaid
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.
578 ../../../Workflow-Corpus-Open-License/nf-core/spatialtranscriptomics
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.
580 ../../../Workflow-Corpus-Open-License/nf-core/eager
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.
582 ../../../Workflow-Corpus-Open-License/nf-core/rnaseq
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.
584 ../../../Workflow-Corpus-Open-License/nf-core/omicsgenetraitassociation
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.
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.
587 ../../../Workflow-Corpus-Open-License/nf-core/vipr
588 ../../../Workflow-Corpus-Open-License/nf-core/methylseq
589 ../../../Workflow-Corpus-Open-License/nf-core/viralintegration
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.
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.
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.
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'.
594 ../../../Workflow-Corpus-Open-License/nf-core/isoseq
595 ../../../Workflow-Corpus-Open-License/nf-core/pathogensurveillance
596 ../../../Workflow-Corpus-Open-License/nf-core/phyloplace
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.
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.
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.
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.
601 ../../../Workflow-Corpus-Open-License/nf-core/fastquorum
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.
603 ../../../Workflow-Corpus-Open-License/nf-core/bamtofastq
604 ../../../Workflow-Corpus-Open-License/nf-core/clipseq
605 ../../../Workflow-Corpus-Open-License/nf-core/neutronstar
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.
607 ../../../Workflow-Corpus-Open-License/nf-core/createtaxdb
608 ../../../Workflow-Corpus-Open-License/nf-core/gwas
609 ../../../Workflow-Corpus-Open-License/nf-core/coproid
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'.
611 ../../../Workflow-Corpus-Open-License/nf-core/sarek
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.
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.
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.
615 ../../../Workflow-Corpus-Open-License/nf-core/proteomicslfq
616 ../../../Workflow-Corpus-Open-License/nf-core/bactmap
617 ../../../Workflow-Corpus-Open-License/nf-core/mnaseseq
618 ../../../Workflow-Corpus-Open-License/nf-core/metapep
619 ../../../Workflow-Corpus-Open-License/nf-core/crisprvar
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()
| combine( ch_db_for_decoy_creation )
| map { it[-1] }
| set {ch_db_for_decoy_creation_or_null}', possibly at line 135.
621 ../../../Workflow-Corpus-Open-License/nf-core/imcyto
622 ../../../Workflow-Corpus-Open-License/andrecossa5/mito_preprocessing
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.
624 ../../../Workflow-Corpus-Open-License/dakoner/nextflow-example
625 ../../../Workflow-Corpus-Open-License/lifebit-ai/DeepVariant
626 ../../../Workflow-Corpus-Open-License/lifebit-ai/roary
627 ../../../Workflow-Corpus-Open-License/lifebit-ai/Plant-RNASeq
628 ../../../Workflow-Corpus-Open-License/lifebit-ai/onemetagenome
629 ../../../Workflow-Corpus-Open-License/jb-adams/variable-length-inputs-nf
630 ../../../Workflow-Corpus-Open-License/JingQiChong/nf_CRACpipeline
631 ../../../Workflow-Corpus-Open-License/juneb4869/new_meripseqpipe
632 ../../../Workflow-Corpus-Open-License/rmhubley/pseudo-it-nextflow
633 ../../../Workflow-Corpus-Open-License/louperelo/longmetarg
634 ../../../Workflow-Corpus-Open-License/j3551ca/BEAST-FLOW
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')
636 ../../../Workflow-Corpus-Open-License/raonyguimaraes/nextflow-hello
637 ../../../Workflow-Corpus-Open-License/MazdaX/nf-cage
638 ../../../Workflow-Corpus-Open-License/qbic-pipelines/rnadeseq
639 ../../../Workflow-Corpus-Open-License/qbic-pipelines/cellranger
640 ../../../Workflow-Corpus-Open-License/CollinsLabBioComp/nextflow-sc_dge
641 ../../../Workflow-Corpus-Open-License/dholab/nf-iWES
642 ../../../Workflow-Corpus-Open-License/avantonder/bovisanalyzer
643 ../../../Workflow-Corpus-Open-License/bigbio/pgdb
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.
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.
646 ../../../Workflow-Corpus-Open-License/cnr-ibba/nf-neestimator
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.
648 ../../../Workflow-Corpus-Open-License/OLC-Bioinformatics/BaitCapture
649 ../../../Workflow-Corpus-Open-License/nvnieuwk/nf-samplesheet-conversion
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'.
651 ../../../Workflow-Corpus-Open-License/chrisjackson-pellicle/paragone-nf
652 ../../../Workflow-Corpus-Open-License/VEuPathDB/marker-gene-analysis-16s-DADA2-nextflow
653 ../../../Workflow-Corpus-Open-License/VEuPathDB/psipred-nextflow
654 ../../../Workflow-Corpus-Open-License/VEuPathDB/dnaseq-nextflow
655 ../../../Workflow-Corpus-Open-License/VEuPathDB/mitoprot-nextflow
656 ../../../Workflow-Corpus-Open-License/VEuPathDB/gpi-anchor-prediction-nextflow
657 ../../../Workflow-Corpus-Open-License/VEuPathDB/hmmer-nextflow
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.
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'
660 ../../../Workflow-Corpus-Open-License/PMCC-BioinformaticsCore/dinoflow
661 ../../../Workflow-Corpus-Open-License/Papatheodorou-Group/BENGAL
662 ../../../Workflow-Corpus-Open-License/OligoGeneticDiseases/oligo-nf
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.
664 ../../../Workflow-Corpus-Open-License/Arcadia-Science/metagenomics
665 ../../../Workflow-Corpus-Open-License/Arcadia-Science/seqqc
666 ../../../Workflow-Corpus-Open-License/ifremer-bioinformatics/samba
667 ../../../Workflow-Corpus-Open-License/dalmolingroup/bulkrna
668 ../../../Workflow-Corpus-Open-License/abyssum/NeoFuse2
669 ../../../Workflow-Corpus-Open-License/dhslab/nf-core-wgsnano
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.
671 ../../../Workflow-Corpus-Open-License/George-Marchment/hackathon
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.
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.
674 ../../../Workflow-Corpus-Open-License/daupt/hello-nextflow
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.
676 ../../../Workflow-Corpus-Open-License/crickbabs/BABS-MNASeqPE
677 ../../../Workflow-Corpus-Open-License/crickbabs/BABS-ATACSeqPE
%% Cell type:code id: tags:
``` python
if(run_analysis_on_corpus):
print(f"Analysed {100-nb_errors/len(workflows)*100:.2f}% ({len(workflows)-nb_errors}) of the workflows succesfully. The others failed.")
```
%% Output
Analysed 75.37% (511) of the workflows succesfully. The others failed.
%% Cell type:markdown id: tags:
## Analysing the results
%% Cell type:code id: tags:
``` python
if(analyse_results):
df = pd.DataFrame(DSL_tab)
df.groupby(["DSL"]).count()
```
%% Cell type:code id: tags:
``` python
if(analyse_results):
def autopct_george(group):
def flatten(l):
return [item for sublist in l for item in sublist]
#https://stackoverflow.com/questions/73616867/pie-chart-from-count-of-values-showing-the-percentage
#https://stackoverflow.com/a/71515035/2901002
def autopct_format(values):
def my_format(pct):
total = sum(values)
val = int(round(pct*total/100.0))
return '{:.1f}%'.format(pct, v=val)
return my_format
return autopct_format(flatten(group.values.tolist()))
group = df.groupby(['DSL']).count()
explode = [0.03]*len(group)
_ = 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 *\[(\d+)\] "
with open('failed_2_analyse.txt') as f:
errors = f.read()
```
%% Cell type:code id: tags:
``` python
dico_nb_errors = {}
for match in re.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."
}
```
%% Cell type:code id: tags:
``` python
df = pd.DataFrame([dico_type_errors, dico_nb_errors]).T
df.columns = ["Error description", "Number of workflows"]
df.to_csv("different_errors_detected.csv", sep='\t', index=False)
df
```
%% Output
Error description Number of workflows
2 Incorrect number of parameters given for a pro... 16
4 Channel trying to be created with a name alrea... 27
6 Multiple channels are given by an emit even th... 1
8 Tried to access an emit even though the elemen... 16
10 Tried to include a file which doesn't exist 14
12 An include was present in a main or subworkflow 1
14 In a pipe operator, the first thing called doe... 11
16 Syntax error in the code (e.g. not the same of... 35
18 Element (process or subworkflow) is expected t... 8
20 A subworkflow either emits nothing or too many... 20
22 A subworkflow or process was defined badly (e.... 10
3 Unknown element used in a pipe operator. 1
5 Ternary conditional operator used with a tuple. 2
9 Tuple associated with a call. 5
......
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