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FIX: join duplication for manta/strelka annotation #1063

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merged 3 commits into from
Jun 2, 2023
Merged

FIX: join duplication for manta/strelka annotation #1063

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cb090b2
fix comment
maxulysse Jun 2, 2023
5e17e25
FIX: join mismatch for annotation
maxulysse Jun 2, 2023
7c83c74
update CHANGELOG
maxulysse Jun 2, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -78,6 +78,7 @@ Bierikjávrre is one of the largest lake in Sarek.
- [#1055](https://github.com/nf-core/sarek/pull/1055) - Fix pattern for fasta file in the json schema
- [#1058](https://github.com/nf-core/sarek/pull/1058) - Fix container declaration for VCFTOOLS as it has been updated in the registry
- [#1062](https://github.com/nf-core/sarek/pull/1062) - Fix automatic restart from steps
- [#1063](https://github.com/nf-core/sarek/pull/1063) - Fix join duplication for manta/strelka

### Removed

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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_single_strelka/main.nf
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Expand Up @@ -42,7 +42,7 @@ workflow BAM_VARIANT_CALLING_SINGLE_STRELKA {
MERGE_STRELKA_GENOME(genome_vcf_to_merge, dict)

// Mix intervals and no_intervals channels together
// Only strelka variant vcf SV should get annotated
// Only strelka variant vcf should get annotated
vcf = Channel.empty().mix(MERGE_STRELKA.out.vcf, vcf.no_intervals)
// add variantcaller to meta map and remove no longer necessary field: num_intervals
.map{ meta, vcf -> [ meta - meta.subMap('num_intervals') + [ variantcaller:'strelka' ], vcf ] }
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2 changes: 1 addition & 1 deletion workflows/sarek.nf
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Expand Up @@ -1040,7 +1040,7 @@ workflow SAREK {
vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[], []]

VCF_ANNOTATE_ALL(
vcf_to_annotate,
vcf_to_annotate.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] },
vep_fasta,
params.tools,
params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}",
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