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Merge pull request #587 from nf-core/new-module-ctat-splicing
New module ctat splicing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| process CTATSPLICING_STARTOCANCERINTRONS { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
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| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/CTAT-SPLICING/ctat_splicing.v0.0.2.simg' : | ||
| 'docker.io/trinityctat/ctat_splicing:0.0.2' }" | ||
|
|
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| input: | ||
| tuple val(meta), path(split_junction), path(junction), path(bam), path(bai) | ||
| tuple val(meta2), path(genome_lib) | ||
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| output: | ||
| tuple val(meta), path("*.cancer_intron_reads.sorted.bam") , emit: cancer_introns_sorted_bam | ||
| tuple val(meta), path("*.cancer_intron_reads.sorted.bam.bai") , emit: cancer_introns_sorted_bai | ||
| tuple val(meta), path("*.gene_reads.sorted.sifted.bam") , emit: gene_reads_sorted_bam | ||
| tuple val(meta), path("*.gene_reads.sorted.sifted.bam.bai") , emit: gene_reads_sorted_bai | ||
| tuple val(meta), path("*.cancer.introns") , emit: cancer_introns | ||
| tuple val(meta), path("*.cancer.introns.prelim") , emit: cancer_introns_prelim | ||
| tuple val(meta), path("*${prefix}.introns") , emit: introns | ||
| tuple val(meta), path("*.introns.for_IGV.bed") , emit: introns_igv_bed, optional: true | ||
| tuple val(meta), path("*.ctat-splicing.igv.html") , emit: igv_html, optional: true | ||
| tuple val(meta), path("*.igv.tracks") , emit: igv_tracks, optional: true | ||
| tuple val(meta), path("*.chckpts") , emit: chckpts | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| def bam_arg = bam ? "--bam_file ${bam}" : "" | ||
| def VERSION = '0.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| def create_index = bam && !bai ? "samtools index ${bam}" : "" | ||
| """ | ||
| ${create_index} | ||
| /usr/local/src/CTAT-SPLICING/STAR_to_cancer_introns.py \\ | ||
| --SJ_tab_file ${split_junction} \\ | ||
| --chimJ_file ${junction} \\ | ||
| ${bam_arg} \\ | ||
| --output_prefix ${prefix} \\ | ||
| --ctat_genome_lib ${genome_lib} \\ | ||
| ${args} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| ctat-splicing: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
|
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = '0.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | ||
| def create_igv_files = args.contains("--vis") ? "touch ${prefix}.introns.for_IGV.bed && touch ${prefix}.ctat-splicing.igv.html && touch ${prefix}.igv.tracks" : "" | ||
| """ | ||
| ${create_igv_files} | ||
| touch ${prefix}.cancer_intron_reads.sorted.bam | ||
| touch ${prefix}.cancer_intron_reads.sorted.bam.bai | ||
| touch ${prefix}.gene_reads.sorted.sifted.bam | ||
| touch ${prefix}.gene_reads.sorted.sifted.bam.bai | ||
| touch ${prefix}.cancer.introns | ||
| touch ${prefix}.cancer.introns.prelim | ||
| touch ${prefix}.introns | ||
| touch ${prefix}.chckpts | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| ctat-splicing: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
| } |
69 changes: 69 additions & 0 deletions
69
modules/local/ctatsplicing/startocancerintrons/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| nextflow_process { | ||
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| name "Test Process CTATSPLICING_STARTOCANCERINTRONS" | ||
| script "../main.nf" | ||
| process "CTATSPLICING_STARTOCANCERINTRONS" | ||
| options "-stub" | ||
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| test("test without BAM") { | ||
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| when { | ||
| params { | ||
| outdir = "tests/results" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:"test"], | ||
| file("test.SJ.out.tab"), | ||
| file("test.Chimeric.out.junctions"), | ||
| [], | ||
| [] | ||
| ] | ||
| input[1] = [ | ||
| [id:"reference"], | ||
| file("ctat_genome_lib") | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.findAll { key, value -> !key.isNumber() }).match() } | ||
| ) | ||
| } | ||
| } | ||
|
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| test("test with BAM") { | ||
|
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| when { | ||
| params { | ||
| outdir = "tests/results" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:"test"], | ||
| file("test.SJ.out.tab"), | ||
| file("test.Chimeric.out.junctions"), | ||
| file("test.Aligned.sortedByCoord.out.bam"), | ||
| [] | ||
| ] | ||
| input[1] = [ | ||
| [id:"reference"], | ||
| file("ctat_genome_lib") | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.findAll { key, value -> !key.isNumber() }).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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