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CAT: Use meta map and supply output file name via modules.config (#1446)
* Use meta map and supply output file name via modules.config * Remove all def declarations to make it work * update tests & remove extra . * fix ze tests * update meta.yml with meta map info * add tag line now that meta is available
This commit is contained in:
FriederikeHanssen
GitHub
parent
e786457fb0
commit
3d31fa4d04
5 changed files with 49 additions and 29 deletions
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@ -1,4 +1,5 @@
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process CAT_CAT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null)
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@ -7,11 +8,10 @@ process CAT_CAT {
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'quay.io/biocontainers/pigz:2.3.4' }"
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input:
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path files_in
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val file_out
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tuple val(meta), path(files_in)
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output:
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path "${file_out}*" , emit: file_out
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tuple val(meta), path("${prefix}"), emit: file_out
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path "versions.yml" , emit: versions
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when:
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@ -29,16 +29,18 @@ process CAT_CAT {
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// | gzipped | ungzipped | zcat | |
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// | ungzipped | gzipped | cat | pigz |
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def in_zip = file_list[0].endsWith('.gz')
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def out_zip = file_out.endsWith('.gz')
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def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
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def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
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// Use input file ending as default
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prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
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out_zip = prefix.endsWith('.gz')
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in_zip = file_list[0].endsWith('.gz')
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command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
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command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
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"""
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$command1 \\
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$args \\
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${file_list.join(' ')} \\
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$command2 \\
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> $file_out
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> ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -12,13 +12,15 @@ tools:
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tool_dev_url: None
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licence: ["GPL-3.0-or-later"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- files_in:
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type: file
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description: List of compressed / uncompressed files
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pattern: "*"
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- file_out:
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type: value
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description: Full name of output file with or without .gz extension
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output:
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- versions:
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@ -32,3 +34,4 @@ output:
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authors:
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- "@erikrikarddaniel"
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- "@FriederikeHanssen"
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@ -3,52 +3,59 @@
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nextflow.enable.dsl = 2
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include { CAT_CAT } from '../../../../modules/cat/cat/main.nf'
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include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/cat/cat/main.nf'
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include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/cat/cat/main.nf'
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workflow test_cat_unzipped_unzipped {
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input = [
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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[ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ]
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]
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CAT_CAT ( input, 'cat.txt' )
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CAT_CAT ( input )
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}
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workflow test_cat_zipped_zipped {
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input = [
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file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
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[ id:'test', single_end:true ], // meta map
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[file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
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]
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CAT_CAT ( input, 'cat.txt.gz' )
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CAT_CAT ( input )
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}
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workflow test_cat_zipped_unzipped {
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input = [
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file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
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[ id:'test', single_end:true ], // meta map
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[file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
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]
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CAT_CAT ( input, 'cat.txt' )
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CAT_ZIPPED_UNZIPPED ( input )
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}
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workflow test_cat_unzipped_zipped {
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input = [
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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[ id:'test', single_end:true ], // meta map
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[file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
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]
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CAT_CAT ( input, 'cat.txt.gz' )
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CAT_UNZIPPED_ZIPPED ( input )
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}
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workflow test_cat_one_file_unzipped_zipped {
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input = [
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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]
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CAT_CAT ( input, 'cat.txt.gz' )
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CAT_UNZIPPED_ZIPPED ( input )
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}
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@ -2,4 +2,12 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: CAT_UNZIPPED_ZIPPED {
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ext.prefix = 'cat.txt.gz'
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}
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withName: CAT_ZIPPED_UNZIPPED {
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ext.prefix = 'cat.txt'
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}
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}
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@ -4,7 +4,7 @@
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- cat
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- cat/cat
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files:
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- path: output/cat/cat.txt
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- path: output/cat/test.fasta
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md5sum: f44b33a0e441ad58b2d3700270e2dbe2
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- name: cat zipped zipped
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@ -13,7 +13,7 @@
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- cat
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- cat/cat
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files:
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- path: output/cat/cat.txt.gz
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- path: output/cat/test.gz
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- name: cat zipped unzipped
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command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
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