From 348cef4816e2353289a4221f3d01829e21b578af Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 7 Sep 2023 14:30:02 +0200 Subject: [PATCH 1/3] Don't pass in intervals file to freec --- CHANGELOG.md | 1 + subworkflows/local/bam_variant_calling_somatic_all/main.nf | 5 ++++- .../local/bam_variant_calling_tumor_only_all/main.nf | 5 +++-- workflows/sarek.nf | 6 ++++-- 4 files changed, 12 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 65bf5219aa..1e7ea80573 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1203](https://github.com/nf-core/sarek/pull/1203) - Fix issue with Singularity containers on test profiles - [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now - [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered +- [#](https://github.com/nf-core/sarek/pull/) - Don't pass in intervals file to ControlFREEC for WGS analysis ### Dependencies diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf index bb98e6c6a1..de32c6afe9 100644 --- a/subworkflows/local/bam_variant_calling_somatic_all/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_all/main.nf @@ -41,6 +41,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { gc_file // channel: [optional] ascat gc content file rt_file // channel: [optional] ascat rt file joint_mutect2 // boolean: [mandatory] [default: false] run mutect2 in joint mode + wes // boolean: [mandatory] [default: false] whether targeted data is processed main: versions = Channel.empty() @@ -94,6 +95,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { length_file = cf_chrom_len ?: fasta_fai + intervals_controlfreec = wes ? intervals_bed_combined : [] + BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC( mpileup_pair, fasta, @@ -102,7 +105,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { dbsnp_tbi, chr_files, mappability, - intervals_bed_combined + intervals_controlfreec ) versions = versions.mix(MPILEUP_NORMAL.out.versions) diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf index 738350713e..2037e49a58 100644 --- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf +++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf @@ -61,7 +61,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { // CONTROLFREEC (depends on MPILEUP) if (tools.split(',').contains('controlfreec')) { - length_file = cf_chrom_len ?: fasta_fai + length_file = cf_chrom_len ?: fasta_fai + intervals_controlfreec = wes ? intervals_bed_combined : [] BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC( // Remap channel to match module/subworkflow @@ -72,7 +73,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { dbsnp_tbi, chr_files, mappability, - intervals_bed_combined + intervals_controlfreec ) versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC.out.versions) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 8bb11326b3..18f1c85878 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -1146,7 +1146,8 @@ workflow SAREK { mappability, pon, pon_tbi, - params.joint_mutect2 + params.joint_mutect2, + params.wes ) // PAIR VARIANT CALLING @@ -1175,7 +1176,8 @@ workflow SAREK { loci_files, gc_file, rt_file, - params.joint_mutect2 + params.joint_mutect2, + params.wes ) // POST VARIANTCALLING From 79c8e16adccf6d3a3bbd50df62f968f7e060c3d7 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Thu, 7 Sep 2023 14:31:31 +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 1e7ea80573..577471f128 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,7 +58,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1203](https://github.com/nf-core/sarek/pull/1203) - Fix issue with Singularity containers on test profiles - [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now - [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered -- [#](https://github.com/nf-core/sarek/pull/) - Don't pass in intervals file to ControlFREEC for WGS analysis +- [#1214](https://github.com/nf-core/sarek/pull/1214) - Don't pass in intervals file to ControlFREEC for WGS analysis ### Dependencies From 4acf21070a8ac0dd8a15c7e10e77320c6849453f Mon Sep 17 00:00:00 2001 From: Rike Date: Thu, 7 Sep 2023 14:59:19 +0200 Subject: [PATCH 3/3] Fix caridanlity --- subworkflows/local/bam_variant_calling_tumor_only_all/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf index 2037e49a58..e6422b7e6c 100644 --- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf +++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf @@ -35,6 +35,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { panel_of_normals // channel: [optional] panel_of_normals panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi joint_mutect2 // boolean: [mandatory] [default: false] run mutect2 in joint mode + wes // boolean: [mandatory] [default: false] whether targeted data is processed main: versions = Channel.empty()