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Fix CENTRIFUGE header modification when --out-fmt turned on #338

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merged 4 commits into from
Jul 28, 2023
Merged

Fix CENTRIFUGE header modification when --out-fmt turned on #338

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9f98ccd
Update CENTRIFUGE module and not by default generate SAM alignments
jfy133 Jul 27, 2023
34273d2
Fix PR number
jfy133 Jul 27, 2023
9f0255b
Update CHANGELOG
jfy133 Jul 27, 2023
3437201
Merge branch 'dev' into centrifuge-fix
jfy133 Jul 27, 2023
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5 changes: 4 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#313](https://github.com/nf-core/taxprofiler/pull/304) Fix pipeline not providing error when database sheet does not have a header (♥ to @noah472 for reporting, fix by @jfy133)
- [#330](https://github.com/nf-core/taxprofiler/pull/330) Added better tagging to allow disambiguation of Kraken2 steps of Kraken2 vs Bracken (♥ to @MajoroMask for requesting, added by @jfy133)
- [#334](https://github.com/nf-core/taxprofiler/pull/334) Increase the memory of the FALCO process to 4GB (fix by @LilyAnderssonLee)
- Improved meta map stability for more robust pipeline resuming (fix by @jfy133)
- [#332](https://github.com/nf-core/taxprofiler/pull/332) Improved meta map stability for more robust pipeline resuming (fix by @jfy133)
- [#338](https://github.com/nf-core/taxprofiler/pull/338) Fixed wrong file 'out' file going to `centrifuge kreport` module (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)

### `Dependencies`

Expand All @@ -46,6 +47,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

- [#338](https://github.com/nf-core/taxprofiler/pull/338) Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, to due to a Centrifuge bug modifying profile header. SAM alignments can still be generated if `--out-fmt` supplied in `database.csv` (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)

## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]

### `Added`
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -559,7 +559,7 @@ process {
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt,sam,gz}'
pattern: '*.{txt,sam,tab,gz}'
]
}

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -42,7 +42,7 @@
},
"centrifuge/centrifuge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "7b0b4276fbad744a69c35d3cbf9d55fdfc9491bd",
"installed_by": ["modules"]
},
"centrifuge/kreport": {
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7 changes: 2 additions & 5 deletions modules/nf-core/centrifuge/centrifuge/main.nf
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9 changes: 7 additions & 2 deletions modules/nf-core/centrifuge/centrifuge/meta.yml
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8 changes: 6 additions & 2 deletions subworkflows/local/profiling.nf
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Expand Up @@ -227,7 +227,7 @@ workflow PROFILING {
db: it[3]
}

CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads )
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )

Expand All @@ -236,7 +236,11 @@ workflow PROFILING {
.filter { meta, db -> meta.tool == 'centrifuge' }
.map { meta, db -> [meta.db_name, meta, db] }

ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.report
// We must combine the _results_ file to get correct output - sending the report file will
// weirdly still produce valid-looking output, however the numbers are nonsense.
// Unfortunately the Centrifuge documentation for this was unclear as to _which_ outfile
// goes into it.
ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.results
.map { meta, profile -> [meta.db_name, meta, profile] }
.combine(ch_database_for_centrifugekreport, by: 0)
.multiMap {
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