Open Alessandro201 opened 1 month ago
Hello,
The workflow NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS is run with 0 exit code, however, while the folder ${params.outdir}/04_reporting/consensus_upset_plots is created, the upset plots are not produced.
NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS
${params.outdir}/04_reporting/consensus_upset_plots
Here is the working directory of the workflow:
{workDir}/work/f5/f4[...]/ ├── .command.begin ├── .command.err ├── .command.log ├── .command.out ├── .command.run ├── .command.sh ├── .command.trace ├── .exitcode ├── {GROUP 1}.macs2.consensus.peak_counts.bed -> {workDir}/work/f1/2eea337cf57ff46f6b3b77d9fb8265/{GROUP 1}.macs2.consensus.peak_counts.bed ├── {GROUP 2}.macs2.consensus.peak_counts.bed -> {workDir}/work/ed/19a8a14d34c607dcdaedd4153f8176/{GROUP 2}.macs2.consensus.peak_counts.bed └── versions.yml
And here is .command.sh:
.command.sh
#!/bin/bash -euo pipefail plot_consensus_peaks.py \ --peaks "*.peaks.bed" \ --outpath . cat <<-END_VERSIONS > versions.yml "NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS": python: $(python --version | grep -E -o "([0-9]{1,}\.)+[0-9]{1,}") numpy: $(python -c 'import numpy; print(numpy.__version__)') pandas: $(python -c 'import pandas; print(pandas.__version__)') upsetplot: $(python -c 'import upsetplot; print(upsetplot.__version__)') END_VERSIONS
After modifying the script: section in modules/local/python/plot_consensus_peaks.nf to:
script:
modules/local/python/plot_consensus_peaks.nf
plot_consensus_peaks.py \ --peaks "*.peak_counts.bed" \ --outpath . cat <<-END_VERSIONS > versions.yml "NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS": python: $(python --version | grep -E -o "([0-9]{1,}\.)+[0-9]{1,}") numpy: $(python -c 'import numpy; print(numpy.__version__)') pandas: $(python -c 'import pandas; print(pandas.__version__)') upsetplot: $(python -c 'import upsetplot; print(upsetplot.__version__)') END_VERSIONS
it works as expected.
nextflow run nf-core/cutandrun -profile singularity -params-file params.yaml --input samplesheet.csv params.yaml input: "./samplesheet.csv" outdir: "./results" genome: "GRCh38" peakcaller: "MACS2,SEACR" dt_calc_all_matrix: true use_control: false skip_igv: true
### Relevant files _No response_ ### System information Nextflow: 24.04.3.5916 Hardware: HPC Executor: PBS Container engine: Singularity OS: Rocky Linux 8.10 kernel 4.18.0 Architecture: x86-64 nf-core/cutandrun: tested with both 3.2.2 and master
Thanks for the fix!
I am having the same issue using release 3.2.2.
Description of the bug
Hello,
The workflow
NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS
is run with 0 exit code, however, while the folder${params.outdir}/04_reporting/consensus_upset_plots
is created, the upset plots are not produced.Here is the working directory of the workflow:
And here is
.command.sh
:After modifying the
script:
section inmodules/local/python/plot_consensus_peaks.nf
to:it works as expected.
Command used and terminal output