Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch
comparison 0.4.2/modules/cat/tables/main.nf @ 0:082e0091e813 draft default tip
planemo upload
| author | galaxytrakr |
|---|---|
| date | Fri, 29 May 2026 13:27:47 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:082e0091e813 |
|---|---|
| 1 process TABLE_SUMMARY { | |
| 2 tag "$table_sum_on" | |
| 3 label 'process_low' | |
| 4 | |
| 5 // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container | |
| 6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 7 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml conda-forge::coreutils" : null) | |
| 8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 9 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : | |
| 10 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" | |
| 11 | |
| 12 input: | |
| 13 tuple val(table_sum_on), path(tables) | |
| 14 | |
| 15 output: | |
| 16 tuple val(table_sum_on), path("*.tblsum.txt"), emit: tblsummed | |
| 17 path "*_mqc.yml" , emit: mqc_yml | |
| 18 path "versions.yml" , emit: versions | |
| 19 | |
| 20 when: | |
| 21 task.ext.when == null || task.ext.when || tables | |
| 22 | |
| 23 script: | |
| 24 def args = task.ext.args ?: '' | |
| 25 def onthese = tables.collect().join('\\n') | |
| 26 """ | |
| 27 filenum="1" | |
| 28 header="" | |
| 29 | |
| 30 echo -e "$onthese" | while read -r file; do | |
| 31 | |
| 32 if [ "\${filenum}" == "1" ]; then | |
| 33 header=\$( head -n1 "\${file}" ) | |
| 34 echo -e "\${header}" > ${table_sum_on}.tblsum.txt | |
| 35 fi | |
| 36 | |
| 37 tail -n+2 "\${file}" >> ${table_sum_on}.tblsum.txt | |
| 38 | |
| 39 filenum=\$((filenum+1)) | |
| 40 done | |
| 41 | |
| 42 create_mqc_data_table.py $table_sum_on ${workflow.manifest.name} | |
| 43 | |
| 44 cat <<-END_VERSIONS > versions.yml | |
| 45 "${task.process}": | |
| 46 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) | |
| 47 python: \$( python --version | sed 's/Python //g' ) | |
| 48 END_VERSIONS | |
| 49 | |
| 50 headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) | |
| 51 tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) | |
| 52 | |
| 53 cat <<-END_VERSIONS >> versions.yml | |
| 54 head: \$headver | |
| 55 tail: \$tailver | |
| 56 END_VERSIONS | |
| 57 """ | |
| 58 } |