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Fix missing GUNC overwriting #514 #515

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merged 6 commits into from
Sep 27, 2023
Merged

Fix missing GUNC overwriting #514 #515

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8dfb907
Fix directory names of GUNC output to prevent overwriting
jfy133 Sep 26, 2023
a2f6168
Update CHANGELOG
jfy133 Sep 26, 2023
5b4be5d
Update OUTPUT docs
jfy133 Sep 26, 2023
f0b09f5
Merge branch 'dev' into fix-gunc-overwriting
jfy133 Sep 27, 2023
2db25be
Update docs/output.md
jfy133 Sep 27, 2023
f9691cf
Merge branch 'dev' into fix-gunc-overwriting
jfy133 Sep 27, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#515](https://github.com/nf-core/mag/pull/515) Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)

### `Dependencies`

## 2.4.0 - 2023-09-26
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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -417,7 +417,7 @@ process {
// Make sure to keep directory in sync with gunc_qc.nf
withName: 'GUNC_RUN' {
publishDir = [
path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.id}" },
path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -426,7 +426,7 @@ process {
// Make sure to keep directory in sync with gunc_qc.nf
withName: 'GUNC_MERGECHECKM' {
publishDir = [
path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.id}" },
path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
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6 changes: 3 additions & 3 deletions docs/output.md
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Expand Up @@ -557,13 +557,13 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
<summary>Output files</summary>

- `GenomeBinning/QC/gunc_summary.tsv`
- `GenomeBinning/QC/gunc_checkm_summary.tsv`
- `GenomeBinning/QC/gunc_checkm_GUNCmmary.tsv`
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- `[gunc-database].dmnd`
- `GUNC/`
- `raw/`
- `[assembler]-[binner]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
- `checkmmerged/`
- `[assembler]-[binner]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)

</details>

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