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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| name: cat_cat | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - conda-forge::pigz=2.3.4 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| process CAT_CAT { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : | ||
| 'biocontainers/pigz:2.3.4' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(files_in) | ||
|
|
||
| output: | ||
| tuple val(meta), path("${prefix}"), emit: file_out | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' | ||
| def file_list = files_in.collect { it.toString() } | ||
|
|
||
| // choose appropriate concatenation tool depending on input and output format | ||
|
|
||
| // | input | output | command1 | command2 | | ||
| // |-----------|------------|----------|----------| | ||
| // | gzipped | gzipped | cat | | | ||
| // | ungzipped | ungzipped | cat | | | ||
| // | gzipped | ungzipped | zcat | | | ||
| // | ungzipped | gzipped | cat | pigz | | ||
|
|
||
| // Use input file ending as default | ||
| prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" | ||
| out_zip = prefix.endsWith('.gz') | ||
| in_zip = file_list[0].endsWith('.gz') | ||
| command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' | ||
| command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : '' | ||
| if(file_list.contains(prefix.trim())) { | ||
| error "The name of the input file can't be the same as for the output prefix in the " + | ||
| "module CAT_CAT (currently `$prefix`). Please choose a different one." | ||
| } | ||
| """ | ||
| $command1 \\ | ||
| $args \\ | ||
| ${file_list.join(' ')} \\ | ||
| $command2 \\ | ||
| > ${prefix} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def file_list = files_in.collect { it.toString() } | ||
| prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" | ||
| if(file_list.contains(prefix.trim())) { | ||
| error "The name of the input file can't be the same as for the output prefix in the " + | ||
| "module CAT_CAT (currently `$prefix`). Please choose a different one." | ||
| } | ||
| """ | ||
| touch $prefix | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
|
|
||
| // for .gz files also include the second to last extension if it is present. E.g., .fasta.gz | ||
| def getFileSuffix(filename) { | ||
| def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ | ||
| return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| name: cat_cat | ||
| description: A module for concatenation of gzipped or uncompressed files | ||
| keywords: | ||
| - concatenate | ||
| - gzip | ||
| - cat | ||
| tools: | ||
| - cat: | ||
| description: Just concatenation | ||
| documentation: https://man7.org/linux/man-pages/man1/cat.1.html | ||
| licence: ["GPL-3.0-or-later"] | ||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - files_in: | ||
| type: file | ||
| description: List of compressed / uncompressed files | ||
| pattern: "*" | ||
| output: | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - file_out: | ||
| type: file | ||
| description: Concatenated file. Will be gzipped if file_out ends with ".gz" | ||
| pattern: "${file_out}" | ||
| authors: | ||
| - "@erikrikarddaniel" | ||
| - "@FriederikeHanssen" | ||
| maintainers: | ||
| - "@erikrikarddaniel" | ||
| - "@FriederikeHanssen" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,178 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process CAT_CAT" | ||
| script "../main.nf" | ||
| process "CAT_CAT" | ||
| tag "modules" | ||
| tag "modules_gallvp" | ||
| tag "cat" | ||
| tag "cat/cat" | ||
|
|
||
| test("test_cat_name_conflict") { | ||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'genome', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert !process.success }, | ||
| { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_cat_unzipped_unzipped") { | ||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'test', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
|
|
||
| test("test_cat_zipped_zipped") { | ||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'test', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| def lines = path(process.out.file_out.get(0).get(1)).linesGzip | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, | ||
| { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_cat_zipped_unzipped") { | ||
| config './nextflow_zipped_unzipped.config' | ||
|
|
||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'test', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("test_cat_unzipped_zipped") { | ||
| config './nextflow_unzipped_zipped.config' | ||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'test', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| def lines = path(process.out.file_out.get(0).get(1)).linesGzip | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, | ||
| { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test_cat_one_file_unzipped_zipped") { | ||
| config './nextflow_unzipped_zipped.config' | ||
| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = | ||
| [ | ||
| [ id:'test', single_end:true ], | ||
| [ | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| then { | ||
| def lines = path(process.out.file_out.get(0).get(1)).linesGzip | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, | ||
| { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} | ||
| ) | ||
| } | ||
| } | ||
| } |
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