Process NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC input file name collision

[AprilJack]

Description of the bug

The pipeline fails at the MultiQC step because of a file name collision. Looking at the work directories, there are multiple files for each of the names, all containing different information.

Command used and terminal output

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~\
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/cutandrun v3.2.2-g6e1125d
----------------------------------------------------
Run Name: nostalgic_franklin

####################################################
## nf-core/cutandrun execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:

Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC (1)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC` input file name collision -- There are multiple input files for each of the following file names: peak_metrics/peak_reprod_perc/LKB1_mqc.tsv, peak_metrics/peak_reprod_perc/AD_mqc.tsv, peak_metrics/peak_reprod_perc/AB_mqc.tsv, peak_metrics/peak_reprod_perc/NT_mqc.tsv


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`



The workflow was completed at 2024-08-29T18:54:23.230205194-07:00 (duration: 8h 41m 30s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/cutandrun -r 3.2.2 -profile singularity -params-file nf-params.json



Pipeline Configuration:
-----------------------
 - revision: 3.2.2
 - runName: nostalgic_franklin
 - containerEngine: singularity
 - launchDir: /240828_cutnrun/nf-core
 - workDir: /240828_cutnrun/nf-core/work
 - projectDir: /home/april/.nextflow/assets/nf-core/cutandrun
 - userName: april
 - profile: singularity
 - configFiles: 
 - input: /240828_cutnrun/nfcore-sample-sheet.csv
 - multiqc_title: shira
 - genome: mm10
 - bowtie2: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/
 - gtf: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
 - spikein_bowtie2: s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/
 - spikein_fasta: s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/WholeGenomeFasta/genome.fa
 - fasta: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa
 - peakcaller: seacr,macs2
 - macs_gsize: 2700000000.0
 - replicate_threshold: 1.0
 - Date Started: 2024-08-29T10:12:52.771916410-07:00
 - Date Completed: 2024-08-29T18:54:23.230205194-07:00
 - Pipeline script file path: /home/april/.nextflow/assets/nf-core/cutandrun/main.nf
 - Pipeline script hash ID: de5b72f091727fd964f53dd974cc3c92
 - Pipeline repository Git URL: https://github.com/nf-core/cutandrun
 - Pipeline repository Git Commit: 6e1125d4fee4ea7c8b70ed836bb0e92a89e3305f
 - Pipeline Git branch/tag: 3.2.2
 - Nextflow Version: 23.04.3
 - Nextflow Build: 5875
 - Nextflow Compile Timestamp: 11-08-2023 18:37 UTC

--
nf-core/cutandrun
https://github.com/nf-core/cutandrun



------------------------------------------------------------------------
##Looking at the .command.sh for one of the samples

#!/bin/bash -euo pipefail
cat AD.v.seacr.consensus.peaks.awk.bed | wc -l | awk -v OFS='   ' '{ print "Peak Count", $1 }' | cat peak_counts_consensus_header.txt - > AD.v_mqc.tsv

cat <<-END_VERSIONS > versions.yml
"NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:CONSENSUS_PEAK_COUNTS":
    bedtools: $(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS

----------------------------------------------------------------------------

Relevant files

No response

System information

Pipeline Configuration:

• revision: 3.2.2
• runName: nostalgic_franklin
• containerEngine: singularity
• launchDir: /240828_cutnrun/nf-core
• workDir: /240828_cutnrun/nf-core/work
• projectDir: /home/april/.nextflow/assets/nf-core/cutandrun
• userName: april
• profile: singularity
• configFiles:
• input: /240828_cutnrun/nfcore-sample-sheet.csv
• multiqc_title: shira
• genome: mm10
• bowtie2: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/
• gtf: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
• spikein_bowtie2: s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/
• spikein_fasta: s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/WholeGenomeFasta/genome.fa
• fasta: s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa
• peakcaller: seacr,macs2
• macs_gsize: 2700000000.0
• replicate_threshold: 1.0
• Date Started: 2024-08-29T10:12:52.771916410-07:00
• Date Completed: 2024-08-29T18:54:23.230205194-07:00
• Pipeline script file path: /home/april/.nextflow/assets/nf-core/cutandrun/main.nf
• Pipeline script hash ID: de5b72f091727fd964f53dd974cc3c92
• Pipeline repository Git URL: https://github.com/nf-core/cutandrun
• Pipeline repository Git Commit: 6e1125d
• Pipeline Git branch/tag: 3.2.2
• Nextflow Version: 23.04.3
• Nextflow Build: 5875
• Nextflow Compile Timestamp: 11-08-2023 18:37 UTC