Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/multiqc/main.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 process MULTIQC { |
| kkonganti@101 | 2 label 'process_low' |
| kkonganti@101 | 3 tag 'MultiQC' |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.12" : null) |
| kkonganti@101 | 6 conda (params.enable_conda ? 'bioconda::multiqc=1.12 conda-forge::spectra conda-forge::lzstring' : null) |
| kkonganti@101 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@101 | 8 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : |
| kkonganti@101 | 9 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 input: |
| kkonganti@101 | 12 path multiqc_files |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 output: |
| kkonganti@101 | 15 path "*multiqc*" |
| kkonganti@101 | 16 path "*multiqc_report.html", emit: report |
| kkonganti@101 | 17 path "*_data" , emit: data |
| kkonganti@101 | 18 path "*_plots" , optional: true, emit: plots |
| kkonganti@101 | 19 path "versions.yml" , emit: versions |
| kkonganti@101 | 20 |
| kkonganti@101 | 21 when: |
| kkonganti@101 | 22 task.ext.when == null || task.ext.when |
| kkonganti@101 | 23 |
| kkonganti@101 | 24 script: |
| kkonganti@101 | 25 def args = task.ext.args ?: '' |
| kkonganti@101 | 26 """ |
| kkonganti@101 | 27 cp ${params.projectconf}${params.fs}multiqc${params.fs}${params.pipeline}_mqc.yml cpipes_mqc_config.yml |
| kkonganti@101 | 28 cp ${params.assetsdir}${params.fs}FDa-Logo-Blue---medium-01.png FDa-Logo-Blue---medium-01.png |
| kkonganti@101 | 29 sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml |
| kkonganti@101 | 30 sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s%Workflow_Output_Placeholder%${params.output}%g' cpipes_mqc_config.yml |
| kkonganti@101 | 31 sed -i -e 's%Workflow_Input_Placeholder%${params.input}%g' cpipes_mqc_config.yml |
| kkonganti@101 | 32 |
| kkonganti@101 | 33 multiqc -c cpipes_mqc_config.yml -f $args . |
| kkonganti@101 | 34 |
| kkonganti@101 | 35 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 36 "${task.process}": |
| kkonganti@101 | 37 multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) |
| kkonganti@101 | 38 END_VERSIONS |
| kkonganti@101 | 39 |
| kkonganti@101 | 40 sedver="" |
| kkonganti@101 | 41 |
| kkonganti@101 | 42 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@101 | 43 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@101 | 44 else |
| kkonganti@101 | 45 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' ) |
| kkonganti@101 | 46 fi |
| kkonganti@101 | 47 |
| kkonganti@101 | 48 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@101 | 49 sed: \$sedver |
| kkonganti@101 | 50 END_VERSIONS |
| kkonganti@101 | 51 """ |
| kkonganti@101 | 52 } |