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Fix AncientDNA results files overwriting #451

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merged 1 commit into from
Jun 7, 2023
Merged

Fix AncientDNA results files overwriting #451

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#438](https://github.com/nf-core/mag/pull/438) - Fixed version inconsistency between conda and containers for GTDBTK_CLASSIFYWF (by @jfy133)
- [#439](https://github.com/nf-core/mag/pull/445) - Fix bug in assembly input (by @prototaxites)
- [#447](https://github.com/nf-core/mag/pull/447) - Remove `default: None` from parameter schema (by @drpatelh)
- [#449](https://github.com/nf-core/mag/pull/447) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133)

### `Dependencies`

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12 changes: 9 additions & 3 deletions conf/modules.config
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Expand Up @@ -477,6 +477,7 @@ process {
}

withName: FREEBAYES {
ext.prefix = { "${meta.assembler}-${meta.id}" }
ext.args = "-p ${params.freebayes_ploidy} -q ${params.freebayes_min_basequality} -F ${params.freebayes_minallelefreq}"
publishDir = [
path: { "${params.outdir}/Ancient_DNA/variant_calling/freebayes" },
Expand All @@ -487,7 +488,7 @@ process {

withName: BCFTOOLS_VIEW {
ext.args = "-v snps,mnps -i 'QUAL>=${params.bcftools_view_high_variant_quality} || (QUAL>=${params.bcftools_view_medium_variant_quality} && FORMAT/AO>=${params.bcftools_view_minimal_allelesupport})'"
ext.prefix = { "${meta.id}.filtered" }
ext.prefix = { "${meta.assembler}-${meta.id}.filtered" }
publishDir = [
path: { "${params.outdir}/Ancient_DNA/variant_calling/filtered" },
mode: params.publish_dir_mode,
Expand All @@ -496,6 +497,7 @@ process {
}

withName: BCFTOOLS_CONSENSUS {
ext.prefix = { "${meta.assembler}-${meta.id}" }
publishDir = [
path: {"${params.outdir}/Ancient_DNA/variant_calling/consensus" },
mode: params.publish_dir_mode,
Expand All @@ -504,6 +506,7 @@ process {
}

withName: BCFTOOLS_INDEX {
ext.prefix = { "${meta.assembler}-${meta.id}" }
ext.args = "-t"
publishDir = [
path: {"${params.outdir}/Ancient_DNA/variant_calling/index" },
Expand All @@ -513,21 +516,24 @@ process {
}

withName: PYDAMAGE_ANALYZE {
ext.prefix = { "${meta.assembler}-${meta.id}" }
publishDir = [
path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.id}" },
path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/" },
mode: params.publish_dir_mode
]
}

withName: PYDAMAGE_FILTER {
ext.prefix = { "${meta.assembler}-${meta.id}" }
ext.args = "-t ${params.pydamage_accuracy}"
publishDir = [
path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.id}" },
path: {"${params.outdir}/Ancient_DNA/pydamage/filter/" },
mode: params.publish_dir_mode
]
}

withName: SAMTOOLS_FAIDX {
ext.prefix = { "${meta.assembler}-${meta.id}" }
publishDir = [
path: {"${params.outdir}/Ancient_DNA/samtools/faidx" },
mode: params.publish_dir_mode,
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10 changes: 5 additions & 5 deletions docs/output.md
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Expand Up @@ -617,9 +617,9 @@ Optional, only running when parameter `-profile ancient_dna` is specified.
<summary>Output files</summary>

- `Ancient_DNA/pydamage/analyze`
- `[sample/group]/pydamage_results/pydamage_results.csv`: PyDamage raw result tabular file in `.csv` format. Format described here: [pydamage.readthedocs.io/en/0.62/output.html](https://pydamage.readthedocs.io/en/0.62/output.html)
- `[assembler]_[sample/group]/pydamage_results/pydamage_results.csv`: PyDamage raw result tabular file in `.csv` format. Format described here: [pydamage.readthedocs.io/en/0.62/output.html](https://pydamage.readthedocs.io/en/0.62/output.html)
- `Ancient_DNA/pydamage/filter`
- `[sample/group]/pydamage_results/pydamage_results.csv`: PyDamage filtered result tabular file in `.csv` format. Format described here: [pydamage.readthedocs.io/en/0.62/output.html](https://pydamage.readthedocs.io/en/0.62/output.html)
- `[assembler]_[sample/group]/pydamage_results/pydamage_results.csv`: PyDamage filtered result tabular file in `.csv` format. Format described here: [pydamage.readthedocs.io/en/0.62/output.html](https://pydamage.readthedocs.io/en/0.62/output.html)

</details>

Expand All @@ -631,11 +631,11 @@ Because of aDNA damage, _de novo_ assemblers sometimes struggle to call a correc
<summary>Output files</summary>

- `variant_calling/consensus`
- `[sample/group].fa`: contigs sequence with re-called consensus from read-to-contig alignment
- `[assembler]_[sample/group].fa`: contigs sequence with re-called consensus from read-to-contig alignment
- `variant_calling/unfiltered`
- `[sample/group].vcf.gz`: raw variant calls of the reads aligned back to the contigs.
- `[assembler]_[sample/group].vcf.gz`: raw variant calls of the reads aligned back to the contigs.
- `variant_calling/filtered`
- `[sample/group].filtered.vcf.gz`: quality filtered variant calls of the reads aligned back to the contigs.
- `[assembler]_[sample/group].filtered.vcf.gz`: quality filtered variant calls of the reads aligned back to the contigs.

</details>

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