diff --git a/CHANGELOG.md b/CHANGELOG.md index 79236097..b61486da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) - Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387) - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) +- Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396) +- Update picard container for `PICARD_COLLECTRNASEQMETRICS` to 3.0.0 [#395](https://github.com/nf-core/rnafusion/pull/395) ### Fixed @@ -23,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed +- `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395) - Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394) ## v2.3.0 = [2022/04/24] @@ -40,6 +43,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results - Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector` - Exit with error when using squid in combination with any ensembl version different from 102 +- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395) + - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation + - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba + - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out + - `fusion-report` index.html file to meta.id_fusionreport_index.html + - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf ### Fixed diff --git a/conf/modules.config b/conf/modules.config index 4bee29b3..b4dc96d6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -36,7 +36,8 @@ process { } withName: ARRIBA_VISUALISATION { - ext.when = { !params.fusioninspector_only && (params.starfusion || params.all) } + ext.when = { !params.fusioninspector_only && (params.starfusion || params.all) } + ext.prefix = { "${meta.id}_combined_fusions_arriba_visualisation" } publishDir = [ path: { "${params.outdir}/arriba_visualisation" }, mode: params.publish_dir_mode, @@ -142,6 +143,7 @@ process { } withName: MEGAFUSION { ext.when = {!params.fusioninspector_only} + ext.prefix = { "${meta.id}_fusion_data" } } @@ -185,14 +187,6 @@ process { ] } - withName: SAMTOOLS_INDEX_FOR_ARRIBA { - publishDir = [ - path: { "${params.outdir}/star_for_arriba" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_INDEX_FOR_STARFUSION { publishDir = [ path: { "${params.outdir}/star_for_starfusion" }, @@ -201,7 +195,7 @@ process { ] } - withName: SAMTOOLS_FAIDX { + withName: SAMTOOLS_FAIDX { publishDir = [ path: { "${params.genomes_base}/ensembl" }, mode: params.publish_dir_mode, @@ -209,15 +203,6 @@ process { ] } - withName: SAMTOOLS_SORT_FOR_ARRIBA { - ext.prefix = { "${meta.id}_sorted" } - publishDir = [ - path: { "${params.outdir}/samtools_sort_for_arriba" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_SORT_FOR_SQUID_CHIMERIC { ext.prefix = { "${meta.id}_chimeric_sorted" } publishDir = [ @@ -229,6 +214,7 @@ process { withName: SAMTOOLS_VIEW_FOR_ARRIBA { ext.args = { "--output-fmt cram" } + ext.prefix = { "${meta.id}_star_for_arriba" } publishDir = [ path: { "${params.outdir}/cram_arriba" }, mode: params.publish_dir_mode, @@ -267,6 +253,7 @@ process { withName: SAMTOOLS_VIEW_FOR_STARFUSION { ext.args = { "--output-fmt cram" } + ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" } publishDir = [ path: { "${params.outdir}/cram_starfusion" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 38ba9c33..162a71b5 100644 --- a/modules.json +++ b/modules.json @@ -32,7 +32,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { @@ -62,7 +62,7 @@ }, "picard/markduplicates": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448", "installed_by": ["modules"] }, "qualimap/rnaseq": { diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 0b18c34a..20db8c2f 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -15,7 +15,7 @@ process FUSIONREPORT { path "versions.yml" , emit: versions tuple val(meta), path("*fusionreport.tsv") , emit: fusion_list tuple val(meta), path("*fusionreport_filtered.tsv") , emit: fusion_list_filtered - tuple val(meta), path("index.html") , emit: report + tuple val(meta), path("*index.html") , emit: report tuple val(meta), path("*_*.html") , optional:true, emit: html tuple val(meta), path("*.csv") , optional:true, emit: csv tuple val(meta), path("*.json") , optional:true, emit: json @@ -37,6 +37,7 @@ process FUSIONREPORT { mv fusion_list.tsv ${prefix}.fusionreport.tsv mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv + mv index.html ${prefix}_fusionreport_index.html [ ! -f fusions.csv ] || mv fusions.csv ${prefix}.fusions.csv [ ! -f fusions.json ] || mv fusions.json ${prefix}.fusions.json @@ -52,7 +53,7 @@ process FUSIONREPORT { """ touch ${prefix}.fusionreport_filtered.tsv touch ${prefix}.fusionreport.tsv - touch index.html + touch ${prefix}_fusionreport_index.html touch AAA_BBB.html touch ${prefix}.fusions.csv touch ${prefix}.fusions.json diff --git a/modules/local/picard/collectrnaseqmetrics/main.nf b/modules/local/picard/collectrnaseqmetrics/main.nf index 5651c6c1..af0b8958 100644 --- a/modules/local/picard/collectrnaseqmetrics/main.nf +++ b/modules/local/picard/collectrnaseqmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=2.27.4" + conda "bioconda::picard=3.0.0 r::r-base" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..3961de60 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test Process FASTQC" + script "modules/nf-core/fastqc/main.nf" + process "FASTQC" + tag "fastqc" + + test("Single-Read") { + + when { + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" + assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") + assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + } + + } + +} diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index facd7efb..ebfa0864 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -30,6 +30,9 @@ process PICARD_MARKDUPLICATES { } else { avail_mem = (task.memory.mega*0.8).intValue() } + + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ picard \\ -Xmx${avail_mem}M \\ @@ -48,6 +51,7 @@ process PICARD_MARKDUPLICATES { stub: def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.bam touch ${prefix}.bam.bai diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 9f770190..36c3924f 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -1,6 +1,4 @@ include { ARRIBA } from '../../modules/nf-core/arriba/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_ARRIBA} from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_FOR_ARRIBA } from '../../modules/nf-core/samtools/sort/main' include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_ARRIBA} from '../../modules/nf-core/samtools/view/main' include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../modules/nf-core/star/align/main' @@ -23,16 +21,7 @@ workflow ARRIBA_WORKFLOW { STAR_FOR_ARRIBA( reads, ch_starindex_ref, ch_gtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '') ch_versions = ch_versions.mix(STAR_FOR_ARRIBA.out.versions) - SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions) - - SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions) - - bam_indexed = SAMTOOLS_SORT_FOR_ARRIBA.out.bam.join(SAMTOOLS_INDEX_FOR_ARRIBA.out.bai) - if (params.arriba_fusions) { - // [meta, reads], fusions -> [meta, fusions] ch_arriba_fusions = reads.combine( Channel.value( file( params.arriba_fusions, checkIfExists: true ) ) ) .map { meta, reads, fusions -> [ meta, fusions ] } ch_arriba_fusion_fail = ch_dummy_file @@ -45,9 +34,9 @@ workflow ARRIBA_WORKFLOW { } if (params.cram.contains('arriba') ){ - SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, []) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) + SAMTOOLS_VIEW_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) + ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) }