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Fixing exome flag with Manta #1149

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merged 6 commits into from
Jul 10, 2023
Merged

Fixing exome flag with Manta #1149

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d986783
update CHANGELOG
maxulysse Jul 10, 2023
e2c8ea8
update manta modules
maxulysse Jul 10, 2023
1a83ae1
better align
maxulysse Jul 10, 2023
aaf3dbc
better selectors
maxulysse Jul 10, 2023
aafbf6f
update CHANGELOG
maxulysse Jul 10, 2023
1aba77f
update CHANGELOG
maxulysse Jul 10, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#1143](https://github.com/nf-core/sarek/pull/1143) - `snpeff_db` is now a string
- [#1145](https://github.com/nf-core/sarek/pull/1145) - Fixed Zenodo links in `README.md` and in `WorkflowMain.groovy`
- [#1149](https://github.com/nf-core/sarek/pull/1149) - Update `Manta` modules and fix usage of exome flag

## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare

Expand Down Expand Up @@ -1217,7 +1218,7 @@ Ruotes is one of the main massif in the Sarek National Park.
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to `GATK4`
- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG`
- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated `Nextflow ``$name` syntax with `withName`
- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated ` Nextflow ``$name ` syntax with `withName`
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### Fixed

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21 changes: 10 additions & 11 deletions conf/modules/manta.config
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Expand Up @@ -14,16 +14,15 @@
// MANTA

process {

withName: 'MANTA.*' {
ext.args = { params.wes ? "--exome" : "" }
ext.prefix = { "${meta.id}.manta" }
ext.when = { params.tools && params.tools.split(',').contains('manta') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/manta/${meta.id}" },
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
]
if (params.tools && params.tools.split(',').contains('manta')) {
withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
ext.args = { params.wes ? "--exome" : "" }
ext.prefix = { "${meta.id}.manta" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/manta/${meta.id}" },
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
]
}
}

}
4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -293,12 +293,12 @@
},
"manta/somatic": {
"branch": "master",
"git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7",
"git_sha": "b178a8cc4b8d38b9dc2d0a1e6a9b63e6786ce263",
"installed_by": ["modules"]
},
"manta/tumoronly": {
"branch": "master",
"git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7",
"git_sha": "b178a8cc4b8d38b9dc2d0a1e6a9b63e6786ce263",
"installed_by": ["modules"]
},
"mosdepth": {
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3 changes: 2 additions & 1 deletion modules/nf-core/manta/somatic/main.nf
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3 changes: 2 additions & 1 deletion modules/nf-core/manta/tumoronly/main.nf
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_germline_manta/main.nf
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@@ -1,4 +1,4 @@
include { MANTA_GERMLINE } from '../../../modules/nf-core/manta/germline/main'
include { MANTA_GERMLINE } from '../../../modules/nf-core/manta/germline/main'

// Seems to be the consensus on upstream modules implementation too
workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_somatic_manta/main.nf
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@@ -1,4 +1,4 @@
include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main'
include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main'

workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
take:
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
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@@ -1,4 +1,4 @@
include { MANTA_TUMORONLY } from '../../../modules/nf-core/manta/tumoronly/main'
include { MANTA_TUMORONLY } from '../../../modules/nf-core/manta/tumoronly/main'

// Seems to be the consensus on upstream modules implementation too
workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
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