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Merge pull request #625 from nf-core/dev
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Patch release 3.0.1
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jfy133 authored Jun 10, 2024
2 parents a50117e + 402020b commit aac4962
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20 changes: 20 additions & 0 deletions CHANGELOG.md
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## 3.0.1 [2024-06-10]

### `Added`

### `Changed`

- [#625](https://github.com/nf-core/mag/pull/625) - Updated link to geNomad database for downloading (reported by @amizeranschi, fix by @jfy133)

### `Fixed`

- [#618](https://github.com/nf-core/mag/pull/618) - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)

### `Dependencies`

| Tool | Previous version | New version |
| ---------- | ---------------- | ----------- |
| Centrifuge | 1.0.4_beta | 1.0.4.1 |

### `Deprecated`

## 3.0.0 - [2024-05-13]

### `Added`
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.0" target="_blank">nf-core/mag</a>
This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.1" target="_blank">nf-core/mag</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/mag/3.0.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/mag/3.0.1/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-mag-methods-description":
order: -1000
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22 changes: 20 additions & 2 deletions conf/modules.config
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Expand Up @@ -222,7 +222,16 @@ process {
]
}

withName: CENTRIFUGE {
withName: CENTRIFUGE_CENTRIFUGE {
publishDir = [
path: { "${params.outdir}/Taxonomy/centrifuge/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.txt"
]
}

withName: CENTRIFUGE_KREPORT {
ext.prefix = { "${meta.id}_kreport" }
publishDir = [
path: { "${params.outdir}/Taxonomy/centrifuge/${meta.id}" },
mode: params.publish_dir_mode,
Expand All @@ -239,7 +248,16 @@ process {
]
}

withName: KRONA {
withName: KREPORT2KRONA_CENTRIFUGE {
publishDir = [
path: { "${params.outdir}/Taxonomy/${meta.classifier}/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.txt",
enabled: false
]
}

withName: KRONA_KTIMPORTTAXONOMY {
publishDir = [
path: { "${params.outdir}/Taxonomy/${meta.classifier}/${meta.id}" },
mode: params.publish_dir_mode,
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7 changes: 4 additions & 3 deletions docs/output.md
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Expand Up @@ -170,9 +170,10 @@ More information on the [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) w
<summary>Output files</summary>

- `Taxonomy/centrifuge/[sample]/`
- `report.txt`: Tab-delimited result file. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for information about the fields
- `kreport.txt`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
- `taxonomy.krona.html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)
- `[sample].kreport.txt`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
- `[sample].report.txt`: Tab-delimited result file. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for information about the fields
- `[sample].results.txt`: Per read taxonomic classification information. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for more details
- `[sample].html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)

</details>

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31 changes: 31 additions & 0 deletions modules.json
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"centrifuge/centrifuge": {
"branch": "master",
"git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012",
"installed_by": ["modules"]
},
"centrifuge/kreport": {
"branch": "master",
"git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012",
"installed_by": ["modules"],
"patch": "modules/nf-core/centrifuge/kreport/centrifuge-kreport.diff"
},
"checkm/lineagewf": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"krakentools/kreport2krona": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"krona/kronadb": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"krona/ktimporttaxonomy": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"maxbin2": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["modules"]
}
}
},
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7 changes: 7 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/environment.yml

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91 changes: 91 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/main.nf

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75 changes: 75 additions & 0 deletions modules/nf-core/centrifuge/centrifuge/meta.yml

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