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Restructure depth results #299

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merged 3 commits into from
May 13, 2022
Merged

Restructure depth results #299

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dc0c5bd
Add extra results folder for depth files
skrakau May 13, 2022
88d46b0
Update docs for new depths results folder
skrakau May 13, 2022
732b71b
Update CHANGELOG
skrakau May 13, 2022
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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

- [#269](https://github.com/nf-core/mag/pull/269),[#283](https://github.com/nf-core/mag/pull/283),[#289](https://github.com/nf-core/mag/pull/289) - Update to nf-core 2.3.2 `TEMPLATE`
- [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint
- [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths` for `[assembler]-[sample/group]-depth.txt.gz`, `bin_depths_summary.tsv` and `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`

### `Fixed`

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12 changes: 10 additions & 2 deletions conf/modules.config
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Expand Up @@ -201,7 +201,15 @@ process {
]
}

withName: 'MAG_DEPTHS_PLOT|MAG_DEPTHS_SUMMARY|BIN_SUMMARY' {
withName: 'MAG_DEPTHS_PLOT|MAG_DEPTHS_SUMMARY' {
publishDir = [
path: { "${params.outdir}/GenomeBinning/depths" },
mode: params.publish_dir_mode,
pattern: "*.{png,tsv}"
]
}

withName: 'BIN_SUMMARY' {
publishDir = [
path: { "${params.outdir}/GenomeBinning" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -363,7 +371,7 @@ process {
}
withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
publishDir = [
path: { "${params.outdir}/GenomeBinning/" },
path: { "${params.outdir}/GenomeBinning/depths" },
mode: params.publish_dir_mode,
pattern: '*-depth.txt.gz'
]
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4 changes: 2 additions & 2 deletions docs/output.md
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Expand Up @@ -261,7 +261,7 @@ Sequencing depth per contig and sample is generated by `jgi_summarize_bam_contig
<details markdown="1">
<summary>Output files</summary>

- `GenomeBinning/`
- `GenomeBinning/depths/`
- `[assembler]-[sample/group]-depth.txt.gz`: Sequencing depth for each contig and sample or group, only for short reads.

</details>
Expand Down Expand Up @@ -334,7 +334,7 @@ For each genome bin the median sequencing depth is computed based on the corresp
<details markdown="1">
<summary>Output files</summary>

- `GenomeBinning/`
- `GenomeBinning/depths/`
- `bin_depths_summary.tsv`: Summary of bin sequencing depths for all samples. Depths are available for samples mapped against the corresponding assembly, i.e. according to the mapping strategy specified with `--binning_map_mode`. Only for short reads.
- `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`: Clustered heatmap showing bin abundances of the assembly across samples. Bin depths are transformed to centered log-ratios and bins as well as samples are clustered by Euclidean distance. Again, sample depths are available according to the mapping strategy specified with `--binning_map_mode`.

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