Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/cat/tables/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 process TABLE_SUMMARY { |
| kkonganti@1 | 2 tag "$table_sum_on" |
| kkonganti@1 | 3 label 'process_low' |
| kkonganti@1 | 4 |
| kkonganti@1 | 5 // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container |
| kkonganti@1 | 6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@1 | 7 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml conda-forge::coreutils" : null) |
| kkonganti@1 | 8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@1 | 9 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : |
| kkonganti@1 | 10 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" |
| kkonganti@1 | 11 |
| kkonganti@1 | 12 input: |
| kkonganti@1 | 13 tuple val(table_sum_on), path(tables) |
| kkonganti@1 | 14 |
| kkonganti@1 | 15 output: |
| kkonganti@1 | 16 tuple val(table_sum_on), path("*.tblsum.txt"), emit: tblsummed |
| kkonganti@1 | 17 path "*_mqc.yml" , emit: mqc_yml |
| kkonganti@1 | 18 path "versions.yml" , emit: versions |
| kkonganti@1 | 19 |
| kkonganti@1 | 20 when: |
| kkonganti@1 | 21 task.ext.when == null || task.ext.when || tables |
| kkonganti@1 | 22 |
| kkonganti@1 | 23 script: |
| kkonganti@1 | 24 def args = task.ext.args ?: '' |
| kkonganti@1 | 25 def onthese = tables.collect().join('\\n') |
| kkonganti@1 | 26 """ |
| kkonganti@1 | 27 filenum="1" |
| kkonganti@1 | 28 header="" |
| kkonganti@1 | 29 |
| kkonganti@1 | 30 echo -e "$onthese" | while read -r file; do |
| kkonganti@1 | 31 |
| kkonganti@1 | 32 if [ "\${filenum}" == "1" ]; then |
| kkonganti@1 | 33 header=\$( head -n1 "\${file}" ) |
| kkonganti@1 | 34 echo -e "\${header}" > ${table_sum_on}.tblsum.txt |
| kkonganti@1 | 35 fi |
| kkonganti@1 | 36 |
| kkonganti@1 | 37 tail -n+2 "\${file}" >> ${table_sum_on}.tblsum.txt |
| kkonganti@1 | 38 |
| kkonganti@1 | 39 filenum=\$((filenum+1)) |
| kkonganti@1 | 40 done |
| kkonganti@1 | 41 |
| kkonganti@1 | 42 create_mqc_data_table.py $table_sum_on ${workflow.manifest.name} |
| kkonganti@1 | 43 |
| kkonganti@1 | 44 cat <<-END_VERSIONS > versions.yml |
| kkonganti@1 | 45 "${task.process}": |
| kkonganti@1 | 46 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) |
| kkonganti@1 | 47 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@1 | 48 END_VERSIONS |
| kkonganti@1 | 49 |
| kkonganti@1 | 50 headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@1 | 51 tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@1 | 52 |
| kkonganti@1 | 53 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@1 | 54 head: \$headver |
| kkonganti@1 | 55 tail: \$tailver |
| kkonganti@1 | 56 END_VERSIONS |
| kkonganti@1 | 57 """ |
| kkonganti@1 | 58 } |