From 6444af7b367e3667fd72eb8ab12ebfc3d1caaeb5 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 25 Jan 2021 09:02:03 +0100 Subject: [PATCH] star module tests --- software/star/align/main.nf | 26 +++++++++++++------------- tests/software/star/main.nf | 18 +++++++++++++++--- 2 files changed, 28 insertions(+), 16 deletions(-) diff --git a/software/star/align/main.nf b/software/star/align/main.nf index 0d465e42..50883aa5 100644 --- a/software/star/align/main.nf +++ b/software/star/align/main.nf @@ -12,30 +12,29 @@ process STAR_ALIGN { saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } // Note: 2.7X indices incompatible with AWS iGenomes. - conda (params.enable_conda ? "bioconda::star=2.6.1d" : null) + conda (params.enable_conda ? 'bioconda::star=2.6.1d' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0" + container 'https://depot.galaxyproject.org/singularity/star:2.6.1d--0' } else { - container "quay.io/biocontainers/star:2.6.1d--0" + container 'quay.io/biocontainers/star:2.6.1d--0' } - input: tuple val(meta), path(reads) path index path gtf output: - tuple val(meta), path("*Aligned.out.bam") , emit: bam - tuple val(meta), path("*Log.final.out") , emit: log_final - tuple val(meta), path("*Log.out") , emit: log_out - tuple val(meta), path("*Log.progress.out"), emit: log_progress - path "*.version.txt" , emit: version + tuple val(meta), path('*Aligned.out.bam') , emit: bam + tuple val(meta), path('*Log.final.out') , emit: log_final + tuple val(meta), path('*Log.out') , emit: log_out + tuple val(meta), path('*Log.progress.out'), emit: log_progress + path '*.version.txt' , emit: version - tuple val(meta), path("*sortedByCoord.out.bam") , optional:true, emit: bam_sorted - tuple val(meta), path("*toTranscriptome.out.bam"), optional:true, emit: bam_transcript - tuple val(meta), path("*fastq.gz") , optional:true, emit: fastq - tuple val(meta), path("*.tab") , optional:true, emit: tab + tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted + tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript + tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq + tuple val(meta), path('*.tab') , optional:true, emit: tab script: def software = getSoftwareName(task.process) @@ -48,6 +47,7 @@ process STAR_ALIGN { --readFilesIn $reads \\ --runThreadN $task.cpus \\ --outFileNamePrefix $prefix. \\ + --outSAMtype BAM Unsorted \\ $ignore_gtf \\ $seq_center \\ $options.args diff --git a/tests/software/star/main.nf b/tests/software/star/main.nf index 7afe36bb..72cdaf53 100644 --- a/tests/software/star/main.nf +++ b/tests/software/star/main.nf @@ -1,9 +1,10 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 - -include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [:] ) -include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [:] ) +def options_align = [args: '--readFilesCommand zcat'] +def options_gg = [args: '--genomeSAindexNbases 9'] +include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align ) +include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg ) workflow test_star_genomegenerate { fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) @@ -11,6 +12,17 @@ workflow test_star_genomegenerate { STAR_GENOMEGENERATE ( fasta, gtf ) } +workflow test_star_alignment_single_end { + fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) + gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) + + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ] + + STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf) +} + // workflow test_star_alignment_single_end { // fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)