From 56828b991776e859c7f3f684e7aa91a9193e26d5 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 5 Aug 2024 12:27:05 +0000 Subject: [PATCH 1/3] remove empty output directories --- CHANGELOG.md | 1 + conf/modules/prepare_genome.config | 8 ++++---- conf/modules/prepare_intervals.config | 12 ++++++------ conf/modules/trimming.config | 4 ++-- 4 files changed, 13 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index de3f559584..9c43b577b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,7 @@ Loametjåhkkå is another one of the main peaks of the Pårte massif. - [#1570](https://github.com/nf-core/sarek/pull/1570) - Remove duplicated notes in FASTQC output docs - [#1596](https://github.com/nf-core/sarek/pull/1596) - Fix haplotypecaller tests - [#1597](https://github.com/nf-core/sarek/pull/1597) - Fix deepvariant tests +- [#](https://github.com/nf-core/sarek/pull/) - Remove empty output directories ### Removed diff --git a/conf/modules/prepare_genome.config b/conf/modules/prepare_genome.config index e54138538c..1f57237be7 100644 --- a/conf/modules/prepare_genome.config +++ b/conf/modules/prepare_genome.config @@ -39,9 +39,9 @@ process { ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/cnvkit" }, + path: { "${params.outdir}/reference" }, pattern: "*{bed}", - saveAs: { params.save_reference || params.build_only_index ? it : null } + saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null } ] } @@ -50,9 +50,9 @@ process { ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference } publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/cnvkit" }, + path: { "${params.outdir}/reference" }, pattern: "*{cnn}", - saveAs: { params.save_reference || params.build_only_index ? it : null } + saveAs: { params.save_reference || params.build_only_index ? "cnvkit/${it}" : null } ] } diff --git a/conf/modules/prepare_intervals.config b/conf/modules/prepare_intervals.config index 77814b5d42..815903b996 100644 --- a/conf/modules/prepare_intervals.config +++ b/conf/modules/prepare_intervals.config @@ -23,18 +23,18 @@ process { withName: 'CREATE_INTERVALS_BED' { publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, + path: { "${params.outdir}/reference" }, pattern: "*bed", - saveAs: { params.save_reference || params.build_only_index ? it : null } + saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null } ] } withName: 'GATK4_INTERVALLISTTOBED' { publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, + path: { "${params.outdir}/reference" }, pattern: "*bed", - saveAs: { params.save_reference || params.build_only_index ? it : null } + saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null } ] } @@ -42,9 +42,9 @@ process { ext.prefix = {"${meta.id}"} publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, + path: { "${params.outdir}/reference" }, pattern: "*bed.gz", - saveAs: { params.save_reference || params.build_only_index ? it : null } + saveAs: { params.save_reference || params.build_only_index ? "intervals/${it}" : null } ] } } diff --git a/conf/modules/trimming.config b/conf/modules/trimming.config index d58fa57b67..5fc6f7646b 100644 --- a/conf/modules/trimming.config +++ b/conf/modules/trimming.config @@ -32,10 +32,10 @@ process { pattern: "*.{html,json,log}" ], [ - path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" }, + path: { "${params.outdir}/preprocessing/" }, mode: params.publish_dir_mode, pattern: "*.fastp.fastq.gz", - saveAs: { params.save_trimmed || params.save_split_fastqs ? it : null } + saveAs: { params.save_trimmed || params.save_split_fastqs ? "fastp/${meta.sample}/${it}" : null } ] ] } From 96b4a879c656af47887899bc433e5aee9d1a23e0 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Mon, 5 Aug 2024 14:29:14 +0200 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9c43b577b7..f3e00d0863 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,7 +40,7 @@ Loametjåhkkå is another one of the main peaks of the Pårte massif. - [#1570](https://github.com/nf-core/sarek/pull/1570) - Remove duplicated notes in FASTQC output docs - [#1596](https://github.com/nf-core/sarek/pull/1596) - Fix haplotypecaller tests - [#1597](https://github.com/nf-core/sarek/pull/1597) - Fix deepvariant tests -- [#](https://github.com/nf-core/sarek/pull/) - Remove empty output directories +- [#1612](https://github.com/nf-core/sarek/pull/1612) - Remove empty output directories ### Removed From e48d9bdb25f0f70f3c2c3943cdddfe35abf05838 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 5 Aug 2024 13:07:26 +0000 Subject: [PATCH 3/3] fix linting --- subworkflows/local/bam_variant_calling_cnvkit/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index 800d4b60d6..20d0fe3fd1 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -37,8 +37,8 @@ workflow BAM_VARIANT_CALLING_CNVKIT { versions = versions.mix(CNVKIT_BATCH.out.versions) versions = versions.mix(CNVKIT_GENEMETRICS.out.versions) - versions = versions.mix( CNVKIT_CALL.out.versions) - versions = versions.mix( CNVKIT_EXPORT.out.versions) + versions = versions.mix(CNVKIT_CALL.out.versions) + versions = versions.mix(CNVKIT_EXPORT.out.versions) emit: cnv_calls_raw = CNVKIT_CALL.out.cns // channel: [ meta, cns ] cnv_calls_export = CNVKIT_EXPORT.out.output // channel: [ meta, export_format ]