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Minor fixes + additional tests #200

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Apr 14, 2019
Merged

Minor fixes + additional tests #200

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9c8aa85
Got rid of weird baseName relict
apeltzer Apr 14, 2019
2bdcb76
Add changelog [skip ci]
apeltzer Apr 14, 2019
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -18,8 +18,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183)
* [#196](https://github.com/nf-core/eager/pull/190) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
* [#196](https://github.com/nf-core/eager/pull/190) - Fix issues with PE data being mapped incompletely
* [#196](https://github.com/nf-core/eager/pull/196) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
* [#196](https://github.com/nf-core/eager/pull/196) - Fix issues with PE data being mapped incompletely
* [#200](https://github.com/nf-core/eager/pull/200) - Fix minor issue with some [typos](https://github.com/nf-core/eager/pull/196)

### `Dependencies`

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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -728,7 +728,7 @@ process bwa {
"""
} else {
//PE collapsed, or SE data
prefix = "${reads}.baseName}"
prefix = "${reads.baseName}"
"""
bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.sai
bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
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