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comparison 0.3.0/modules/multiqc/main.nf @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
parents
children 8d7f482c64de
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91:046e57368d3b 92:295c2597a475
1 process MULTIQC {
2 label 'process_low'
3 tag 'MultiQC'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.12" : null)
6 conda (params.enable_conda ? 'bioconda::multiqc=1.12 conda-forge::spectra conda-forge::lzstring' : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
9 'quay.io/biocontainers/multiqc:1.12--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" , optional:true, emit: plots
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 cp ${params.assetsdir}${params.fs}FDa-Logo-Blue---medium-01.png FDa-Logo-Blue---medium-01.png
29 sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml
30 sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s%Workflow_Output_Placeholder%${params.output}%g' cpipes_mqc_config.yml
31 sed -i -e 's%Workflow_Input_Placeholder%${params.input}%g' cpipes_mqc_config.yml
32
33 multiqc -c cpipes_mqc_config.yml -f $args .
34
35 cat <<-END_VERSIONS > versions.yml
36 "${task.process}":
37 multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
38 END_VERSIONS
39
40 sedver=""
41
42 if [ "${workflow.containerEngine}" != "null" ]; then
43 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
44 else
45 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
46 fi
47
48 cat <<-END_VERSIONS >> versions.yml
49 sed: \$sedver
50 END_VERSIONS
51 """
52 }