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Replace local version of sentieon-locuscollector and sentieon-dedup #401

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merged 5 commits into from
Aug 14, 2023
Merged

Replace local version of sentieon-locuscollector and sentieon-dedup #401

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864e2e9
Replace local version of sentieon-locuscollector and sentieon-dedup w…
asp8200 Aug 14, 2023
e887f51
The new modules
asp8200 Aug 14, 2023
08a86ec
Remove includes of old modules
asp8200 Aug 14, 2023
64b7a8d
Delete legacy reference to SENTIEON_LOCUSCOLLECTOR.out.versions
asp8200 Aug 14, 2023
5e7fce7
Update changelog
asp8200 Aug 14, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Installed the nf-core version of the sentieon/bwamem module [#398](https://github.com/nf-core/raredisease/pull/398)
- Installed the nf-core version of the sentieon/readwriter module [#399](https://github.com/nf-core/raredisease/pull/399)
- Installed the nf-core version of the sentieon/datametrics module [#400](https://github.com/nf-core/raredisease/pull/400)
- Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector [#401](https://github.com/nf-core/raredisease/pull/401)

### `Fixed`

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4 changes: 0 additions & 4 deletions conf/modules/align_sentieon.config
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Expand Up @@ -34,10 +34,6 @@ process {
ext.prefix = { "${meta.id}_merged" }
}

withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_LOCUSCOLLECTOR' {
ext.prefix = { "${meta.id}_locuscollector" }
}

withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
ext.args = { $params.rmdup ? "--rmdup" : '' }
ext.prefix = { "${meta.id}_dedup" }
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5 changes: 5 additions & 0 deletions modules.json
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Expand Up @@ -355,6 +355,11 @@
"git_sha": "127edadc279e19da093fdd513926c6cdee82c306",
"installed_by": ["modules"]
},
"sentieon/dedup": {
"branch": "master",
"git_sha": "915a0b16ba3e40ef59e7b44843b3118e17a9c906",
"installed_by": ["modules"]
},
"sentieon/readwriter": {
"branch": "master",
"git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",
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60 changes: 0 additions & 60 deletions modules/local/sentieon/dedup.nf
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52 changes: 0 additions & 52 deletions modules/local/sentieon/locuscollector.nf
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86 changes: 86 additions & 0 deletions modules/nf-core/sentieon/dedup/main.nf
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88 changes: 88 additions & 0 deletions modules/nf-core/sentieon/dedup/meta.yml
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13 changes: 2 additions & 11 deletions subworkflows/local/alignment/align_sentieon.nf
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Expand Up @@ -4,8 +4,7 @@

include { SENTIEON_BWAMEM } from '../../../modules/nf-core/sentieon/bwamem/main'
include { SENTIEON_DATAMETRICS } from '../../../modules/nf-core/sentieon/datametrics/main'
include { SENTIEON_LOCUSCOLLECTOR } from '../../../modules/local/sentieon/locuscollector'
include { SENTIEON_DEDUP } from '../../../modules/local/sentieon/dedup'
include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main'
include { SENTIEON_BQSR } from '../../../modules/local/sentieon/bqsr'
include { SENTIEON_READWRITER } from '../../../modules/nf-core/sentieon/readwriter/main'
workflow ALIGN_SENTIEON {
Expand Down Expand Up @@ -45,14 +44,7 @@ workflow ALIGN_SENTIEON {

SENTIEON_DATAMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai )

SENTIEON_LOCUSCOLLECTOR ( ch_bam_bai )

ch_bam_bai
.join(SENTIEON_LOCUSCOLLECTOR.out.score, failOnMismatch:true, failOnDuplicate:true)
.join(SENTIEON_LOCUSCOLLECTOR.out.score_idx, failOnMismatch:true, failOnDuplicate:true)
.set { ch_bam_bai_score }

SENTIEON_DEDUP ( ch_bam_bai_score, ch_genome_fasta, ch_genome_fai )
SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai )

if (params.variant_caller == "sentieon") {
SENTIEON_DEDUP.out.bam
Expand All @@ -67,7 +59,6 @@ workflow ALIGN_SENTIEON {

ch_versions = ch_versions.mix(SENTIEON_BWAMEM.out.versions.first())
ch_versions = ch_versions.mix(SENTIEON_DATAMETRICS.out.versions.first())
ch_versions = ch_versions.mix(SENTIEON_LOCUSCOLLECTOR.out.versions.first())
ch_versions = ch_versions.mix(SENTIEON_DEDUP.out.versions.first())

emit:
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