From 260e92720c1a26f7d9f4feacd0ebb2a064f8d9b2 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Sun, 14 May 2023 18:46:58 +0000 Subject: [PATCH 1/5] fix snps_resource_label and indels_resource_label --- subworkflows/local/bam_joint_calling_germline_gatk/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf index 858cbec644..c74c7a5199 100644 --- a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf +++ b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf @@ -56,8 +56,8 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK { MERGE_GENOTYPEGVCFS(gvcf_to_merge, dict.map{ it -> [ [ id:'dict' ], it ] } ) vqsr_input = MERGE_GENOTYPEGVCFS.out.vcf.join(MERGE_GENOTYPEGVCFS.out.tbi, failOnDuplicate: true) - indels_resource_label = known_indels_vqsr.mix(dbsnp_vqsr).collect() - snps_resource_label = known_snps_vqsr.mix(dbsnp_vqsr).collect() + snps_resource_label = [known_snps_vqsr, dbsnp_vqsr] + indels_resource_label = [known_indels_vqsr, dbsnp_vqsr] // Recalibrate INDELs and SNPs separately VARIANTRECALIBRATOR_INDEL( From 46b20e9348862a9f77590b53e5f4a04f9d5ed13c Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 15 May 2023 09:40:37 +0000 Subject: [PATCH 2/5] Again trying to get mix operator working with known_indels_vqsr known_snps_vqsr and dbsnp_vqsr --- subworkflows/local/bam_joint_calling_germline_gatk/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf index c74c7a5199..858cbec644 100644 --- a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf +++ b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf @@ -56,8 +56,8 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK { MERGE_GENOTYPEGVCFS(gvcf_to_merge, dict.map{ it -> [ [ id:'dict' ], it ] } ) vqsr_input = MERGE_GENOTYPEGVCFS.out.vcf.join(MERGE_GENOTYPEGVCFS.out.tbi, failOnDuplicate: true) - snps_resource_label = [known_snps_vqsr, dbsnp_vqsr] - indels_resource_label = [known_indels_vqsr, dbsnp_vqsr] + indels_resource_label = known_indels_vqsr.mix(dbsnp_vqsr).collect() + snps_resource_label = known_snps_vqsr.mix(dbsnp_vqsr).collect() // Recalibrate INDELs and SNPs separately VARIANTRECALIBRATOR_INDEL( From 00aafa5cb62ad1c52fdc5fe1c297f541bc2fcc2a Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 15 May 2023 09:41:18 +0000 Subject: [PATCH 3/5] Trying to make sure that dbsnp_vqsr known_indels_vqsr and known_snps_vqsr are channels and not strings --- workflows/sarek.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 73f563e8f7..767fc7790f 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -153,9 +153,9 @@ pon = params.pon ? Channel.fromPath(params.pon).co // Initialize value channels based on params, defined in the params.genomes[params.genome] scope ascat_genome = params.ascat_genome ?: Channel.empty() -dbsnp_vqsr = params.dbsnp_vqsr ?: Channel.empty() -known_indels_vqsr = params.known_indels_vqsr ?: Channel.empty() -known_snps_vqsr = params.known_snps_vqsr ?: Channel.empty() +dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() +known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() +known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() snpeff_db = params.snpeff_db ?: Channel.empty() vep_cache_version = params.vep_cache_version ?: Channel.empty() vep_genome = params.vep_genome ?: Channel.empty() From 3dfe4d6b54df145c380f26e77d5446e4c87391cb Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 15 May 2023 11:44:28 +0000 Subject: [PATCH 4/5] Fixing copy-paste mistake --- workflows/sarek.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 767fc7790f..8fb685ac8f 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -153,8 +153,8 @@ pon = params.pon ? Channel.fromPath(params.pon).co // Initialize value channels based on params, defined in the params.genomes[params.genome] scope ascat_genome = params.ascat_genome ?: Channel.empty() -dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() -known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() +dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty() +known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty() known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() snpeff_db = params.snpeff_db ?: Channel.empty() vep_cache_version = params.vep_cache_version ?: Channel.empty() From c026ee3480b9ef5a619348676f908540c65f9f5f Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 16 May 2023 08:45:56 +0000 Subject: [PATCH 5/5] Updating changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2588c30831..f23cf0aeb4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility - [#998](https://github.com/nf-core/sarek/pull/998) - Remove parallelization within a sample for `Manta` - [#1014](https://github.com/nf-core/sarek/pull/1014) - Fix calls to `ensemblvep` and `snpeff` containers +- [#1022](https://github.com/nf-core/sarek/pull/1022) - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.) ### Deprecated