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FIX: fix kraken file naming #791

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merged 3 commits into from
Sep 9, 2021
Merged

FIX: fix kraken file naming #791

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dd5a4a8
Replace tokenize to basename
jfy133 Sep 9, 2021
d3a4258
Update CHANGELOG.md
jfy133 Sep 9, 2021
82cc021
Remove NF warn message and fix baseName
jfy133 Sep 9, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Updated workflow diagrams to reflect latest functionality
- [#787](https://github.com/nf-core/eager/issues/787) Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
- Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
- [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them

### `Dependencies`

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6 changes: 3 additions & 3 deletions main.nf
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Expand Up @@ -237,12 +237,12 @@ if ( !params.clip_adapters_list ) {
Channel
.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
.ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
.into {ch_adapterlist}
.set {ch_adapterlist}
} else {
Channel
.fromPath("${params.clip_adapters_list}", checkIfExists: true)
.ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
.into {ch_adapterlist}
.set {ch_adapterlist}
}


Expand Down Expand Up @@ -2977,7 +2977,7 @@ process kraken {
tuple prefix, path("*.kraken2_report") into ch_kraken_report, ch_kraken_for_multiqc

script:
prefix = fastq.toString().tokenize('.')[0]
prefix = fastq.baseName
out = prefix+".kraken.out"
kreport = prefix+".kraken2_report"
kreport_old = prefix+".kreport"
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