From 5ac371d78794c3ede0be459ec7a5cf61bf3feac9 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 21 Mar 2024 07:37:59 +0000 Subject: [PATCH 1/3] Adding .collect() in the construction of the channels dict and fasta_fai --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 8658006454..4c6e10416d 100644 --- a/main.nf +++ b/main.nf @@ -148,9 +148,9 @@ workflow NFCORE_SAREK { // Gather built indices or get them from the params // Built from the fasta file: - dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] } + dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict - fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai) + fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : PREPARE_GENOME.out.fasta_fai bwa = params.bwa ? Channel.fromPath(params.bwa).collect() : PREPARE_GENOME.out.bwa From 5bd985625a03ccd701a74df2b327266c3381f25e Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 21 Mar 2024 07:40:09 +0000 Subject: [PATCH 2/3] Adding ascat_loci_gc in input definition for SAMPLESHEET_TO_CHANNEL --- subworkflows/local/samplesheet_to_channel/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/samplesheet_to_channel/main.nf b/subworkflows/local/samplesheet_to_channel/main.nf index 985924efa8..37daa1322a 100644 --- a/subworkflows/local/samplesheet_to_channel/main.nf +++ b/subworkflows/local/samplesheet_to_channel/main.nf @@ -5,6 +5,7 @@ workflow SAMPLESHEET_TO_CHANNEL{ aligner // ascat_alleles // ascat_loci // + ascat_loci_gc // ascat_loci_rt // bcftools_annotations // bcftools_annotations_tbi // @@ -306,5 +307,3 @@ def flowcellLaneFromFastq(path) { } return fcid } - - From 4575cbab5415212f62e2e929343b04b3859f2d58 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Thu, 21 Mar 2024 07:40:56 +0000 Subject: [PATCH 3/3] Adding params.ascat_loci_gc in call to SAMPLESHEET_TO_CHANNEL --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index cadbc48430..afd58a8cc2 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -135,6 +135,7 @@ if (params.tools && (params.tools.split(',').contains('vep') || params.tools. params.aligner, params.ascat_alleles, params.ascat_loci, + params.ascat_loci_gc, params.ascat_loci_rt, params.bcftools_annotations, params.bcftools_annotations_tbi,