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Make target bed file optional for WGS mode #395

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merged 5 commits into from
Aug 4, 2023
Merged

Make target bed file optional for WGS mode #395

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1b0773f
update configs
ramprasadn Aug 1, 2023
adf3ab9
Merge branch 'dev' of github.com:nf-core/raredisease into update-config
ramprasadn Aug 1, 2023
8a6c184
update changelog
ramprasadn Aug 1, 2023
0b083ee
fix typo
ramprasadn Aug 1, 2023
aea0b73
Merge branch 'dev' into update-config
ramprasadn Aug 4, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- Invalid GATK4 container which caused incorrect singularity downloads with nf-core download [nf-core/modules #3668](https://github.com/nf-core/modules/issues/3668)
- Make the default cram prefix same as markduplicates prefix [#392](https://github.com/nf-core/raredisease/pull/392)
- Make target bed file optional for WGS mode (Issue [#375](https://github.com/nf-core/raredisease/issues/375)) [#395](https://github.com/nf-core/raredisease/pull/395)
- Added constraints to block the pipeline from running CollectWgsMetrics on WES samples [#396](https://github.com/nf-core/raredisease/pull/396)

## v1.1.1 - Abu (Patch) [2023-07-26]
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10 changes: 5 additions & 5 deletions conf/modules/prepare_references.config
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Expand Up @@ -86,28 +86,28 @@ process {
}

withName: '.*PREPARE_REFERENCES:TABIX_PT' {
ext.when = { params.target_bed && params.target_bed.endsWith(".gz") }
ext.when = { !params.target_bed.equals(null) && params.target_bed.endsWith(".gz") }
}

withName: '.*PREPARE_REFERENCES:TABIX_PBT' {
ext.when = { params.target_bed && !params.target_bed.endsWith(".gz") }
ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") }
}

withName: '.*PREPARE_REFERENCES:GATK_BILT' {
ext.when = { params.target_bed }
ext.when = { !params.target_bed.equals(null) }
ext.prefix = { "${meta.id}_target" }
}

withName: '.*PREPARE_REFERENCES:GATK_ILT' {
ext.when = { params.target_bed }
ext.when = { !params.target_bed.equals(null) }
ext.args = { "--PADDING ${params.bait_padding} -SUBDIVISION_MODE INTERVAL_SUBDIVISION --SCATTER_COUNT 2" }
publishDir = [
enabled: false
]
}

withName: '.*PREPARE_REFERENCES:CAT_CAT_BAIT' {
ext.when = { params.target_bed }
ext.when = { !params.target_bed.equals(null) }
ext.prefix = { "${meta.id}" }
}

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2 changes: 1 addition & 1 deletion conf/modules/qc_bam.config
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Expand Up @@ -29,7 +29,7 @@ process {
}

withName: '.*QC_BAM:PICARD_COLLECTHSMETRICS' {
ext.when = { params.target_bed }
ext.when = { !params.target_bed.equals(null) }
ext.prefix = { "${meta.id}_hsmetrics" }
}

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