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Bracken output report addition #379

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merged 13 commits into from
Oct 1, 2023
Merged

Bracken output report addition #379

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d1f82f3
Merge pull request #362 from nf-core/dev
LilyAnderssonLee Sep 19, 2023
ee58c4d
added corrected kraken2 report as output from bracken
hkaspersen Sep 20, 2023
c15d035
corrected bracken report output definition
hkaspersen Sep 21, 2023
6a5719c
added line for changes to output
hkaspersen Sep 21, 2023
5f9bfdb
Merge branch 'dev' into bracken_output_report_fix
jfy133 Sep 21, 2023
2f2224e
updated bracken module
hkaspersen Sep 29, 2023
5272ea4
Merge pull request #1 from hkaspersen/master
hkaspersen Sep 29, 2023
89f9051
corrected bracken output glob
hkaspersen Sep 30, 2023
2c8ec49
Merge branch 'bracken_output_report_fix' of github.com:hkaspersen/tax…
hkaspersen Sep 30, 2023
0033280
Merge branch 'dev' into bracken_output_report_fix
jfy133 Oct 1, 2023
a29fa7d
Update conf/modules.config
jfy133 Oct 1, 2023
1dd9144
Update output.md
jfy133 Oct 1, 2023
e6c2cf9
Apply suggestions from code review
jfy133 Oct 1, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#379](https://github.com/nf-core/taxprofiler/pull/379) Added support for previously missing Bracken-corrected Kraken2 report as output (added by @hkaspersen)
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- [#380](https://github.com/nf-core/taxprofiler/pull/380) Updated to nf-core pipeline template v2.10 (added by @LilyAnderssonLee & @sofstam)

### `Fixed`
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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -471,8 +471,8 @@ process {
publishDir = [
path: { "${params.outdir}/bracken/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.tsv'
]
pattern: '*{.tsv,.txt}'
]
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}

withName: BRACKEN_COMBINEBRACKENOUTPUTS {
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -27,7 +27,7 @@
},
"bracken/bracken": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "093e35505936bce5127e1d14966b6cac91cd137f",
"installed_by": ["modules"]
},
"bracken/combinebrackenoutputs": {
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3 changes: 2 additions & 1 deletion modules/nf-core/bracken/bracken/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/bracken/bracken/meta.yml
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