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Remove candidates from manta publishdir and tests #608

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Jun 27, 2022
Merged

Remove candidates from manta publishdir and tests #608

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cad1318
Removed candidates from manta publishdir and tests
WackerO Jun 27, 2022
d09b970
updated changelog
WackerO Jun 27, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -69,6 +69,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
- [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
- [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta

### Fixed

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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -632,7 +632,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/manta" },
pattern: "*{vcf.gz,vcf.gz.tbi}"
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
]
}
withName: 'MERGE_MANTA_DIPLOID' {
Expand All @@ -651,7 +651,7 @@ process{
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/" },
pattern: "*{vcf.gz,vcf.gz.tbi}",
pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}",
saveAs: { meta.num_intervals > 1 ? null : "manta/${it}" }
]
}
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36 changes: 4 additions & 32 deletions tests/test_tools.yml
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Expand Up @@ -323,10 +323,6 @@
- manta
- variant_calling
files:
- path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi

Expand All @@ -338,10 +334,6 @@
- no_intervals
- variant_calling
files:
- path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
- path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi

Expand All @@ -352,10 +344,6 @@
- tumor_only
- variant_calling
files:
- path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi

Expand All @@ -367,10 +355,6 @@
- tumor_only
- variant_calling
files:
- path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
- path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi

Expand All @@ -381,18 +365,12 @@
- somatic
- variant_calling
files:
- path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi

- name: Run variant calling on somatic sample with manta without intervals
command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals
Expand All @@ -402,18 +380,12 @@
- somatic
- variant_calling
files:
- path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
- path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_small_indels.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.candidate_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
- path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi

- name: Run variant calling on tumoronly sample with mutect2
command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mutect2
Expand Down