Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/modules/multiqc/main.nf @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process MULTIQC {
2 label 'process_micro'
3 tag 'MultiQC'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.19" : null)
6 conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
9 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
10
11 input:
12 path multiqc_files
13
14 output:
15 path "*multiqc*"
16 path "*multiqc_report.html", emit: report
17 path "*_data" , emit: data
18 path "*_plots" , emit: plots, optional: true
19 path "versions.yml" , emit: versions
20
21 when:
22 task.ext.when == null || task.ext.when
23
24 script:
25 def args = task.ext.args ?: ''
26 """
27 cp ${params.projectconf}${params.fs}multiqc${params.fs}${params.pipeline}_mqc.yml cpipes_mqc_config.yml
28 sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml
29 sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s|Workflow_Output_Placeholder|${params.output}|g' cpipes_mqc_config.yml
30 sed -i -e 's|Workflow_Input_Placeholder|${params.input}|g' cpipes_mqc_config.yml
31
32 if [ -n "\$(ls *filtlong.log 2> /dev/null)" ]; then
33 sed -i -e 's%,%%g' *filtlong.log
34 fi
35
36 multiqc --interactive -c cpipes_mqc_config.yml -f $args .
37
38 cat <<-END_VERSIONS > versions.yml
39 "${task.process}":
40 multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
41 END_VERSIONS
42
43 sedver=""
44
45 if [ "${workflow.containerEngine}" != "null" ]; then
46 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
47 else
48 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
49 fi
50
51 cat <<-END_VERSIONS >> versions.yml
52 sed: \$sedver
53 END_VERSIONS
54 """
55 }