From 82360dee8c22ac6cd9ffd75ddf7f2d7b6a56a094 Mon Sep 17 00:00:00 2001 From: Raquel Manzano <36073691+RaqManzano@users.noreply.github.com> Date: Tue, 23 Jul 2024 08:20:24 +0100 Subject: [PATCH 1/3] Update somatic vc subworkflow sage and manta Sage throws an error when resource files are not provided because and manta subworkflow needed to be updated. --- .../local/bam_variant_calling_somatic_sage/main.nf | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_somatic_sage/main.nf b/subworkflows/local/bam_variant_calling_somatic_sage/main.nf index 0fb0b7d2..2cdeb9ec 100644 --- a/subworkflows/local/bam_variant_calling_somatic_sage/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_sage/main.nf @@ -43,12 +43,17 @@ workflow BAM_VARIANT_CALLING_SOMATIC_SAGE { cram_intervals = cram.combine(intervals) // Move num_intervals to meta map and reorganize channel for SAGE module .map{ meta, cram1, crai1, cram2, crai2, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram1, crai1, cram2, crai2, intervals ]} + + // init resources + sage_highconfidence = params.sage_highconfidence ? Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([]) + sage_actionablepanel = params.sage_actionablepanel ? Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([]) + sage_knownhotspots = params.sage_knownhotspots ? Channel.fromPath(params.sage_knownhotspots).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([]) SAGE( cram_intervals, sage_ensembl, - Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] }, - Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] }, - Channel.fromPath(params.sage_knownhotspots).collect().map{ it -> [ [ id:it[0].baseName ], it ] }, + sage_highconfidence, + sage_actionablepanel, + sage_knownhotspots, fasta, fasta_fai, dict) From 3e05ea9a080f8d4df2414bb9ac678a5f58a3893b Mon Sep 17 00:00:00 2001 From: Raquel Manzano Date: Tue, 23 Jul 2024 08:25:56 +0100 Subject: [PATCH 2/3] prettier, eclint and manta fix --- .../local/bam_variant_calling_somatic_manta/main.nf | 6 +++--- subworkflows/local/bam_variant_calling_somatic_sage/main.nf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf index 7eb5e668..e57b4dab 100644 --- a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf @@ -9,8 +9,8 @@ include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main' workflow BAM_VARIANT_CALLING_SOMATIC_MANTA { take: cram // channel: [mandatory] [ meta, cram1, crai1, cram2, crai2 ] - fasta // channel: [mandatory] [ fasta ] - fasta_fai // channel: [mandatory] [ fasta_fai ] + fasta // channel: [mandatory] [ meta, fasta ] + fasta_fai // channel: [mandatory] [ meta, fasta_fai ] intervals // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals main: @@ -24,7 +24,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA { [it[0], it[1], it[2], it[3], it[4], bed_gz, bed_tbi] } - MANTA_SOMATIC(cram_intervals, fasta, fasta_fai) + MANTA_SOMATIC(cram_intervals, fasta, fasta_fai. []) candidate_small_indels_vcf = MANTA_SOMATIC.out.candidate_small_indels_vcf candidate_small_indels_vcf_tbi = MANTA_SOMATIC.out.candidate_small_indels_vcf_tbi diff --git a/subworkflows/local/bam_variant_calling_somatic_sage/main.nf b/subworkflows/local/bam_variant_calling_somatic_sage/main.nf index 2cdeb9ec..67b605a9 100644 --- a/subworkflows/local/bam_variant_calling_somatic_sage/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_sage/main.nf @@ -43,7 +43,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_SAGE { cram_intervals = cram.combine(intervals) // Move num_intervals to meta map and reorganize channel for SAGE module .map{ meta, cram1, crai1, cram2, crai2, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram1, crai1, cram2, crai2, intervals ]} - + // init resources sage_highconfidence = params.sage_highconfidence ? Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([]) sage_actionablepanel = params.sage_actionablepanel ? Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([]) From 923e8973360bdedddcfa661fedff3b91f4552006 Mon Sep 17 00:00:00 2001 From: Raquel Manzano Date: Tue, 23 Jul 2024 08:35:12 +0100 Subject: [PATCH 3/3] fix typo --- subworkflows/local/bam_variant_calling_somatic_manta/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf index e57b4dab..f6720c54 100644 --- a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf @@ -24,7 +24,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA { [it[0], it[1], it[2], it[3], it[4], bed_gz, bed_tbi] } - MANTA_SOMATIC(cram_intervals, fasta, fasta_fai. []) + MANTA_SOMATIC(cram_intervals, fasta, fasta_fai, []) candidate_small_indels_vcf = MANTA_SOMATIC.out.candidate_small_indels_vcf candidate_small_indels_vcf_tbi = MANTA_SOMATIC.out.candidate_small_indels_vcf_tbi