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comparison 0.5.0/modules/cat/tables/main.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
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 }