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Bedtools fix #518

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Merged
jfy133 merged 5 commits into from
Jul 20, 2020
Merged

Bedtools fix #518

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3930cd8
Add bedtools to address https://github.com/nf-core/eager/issues/516
jfy133 Jul 17, 2020
7a1c95f
Make ignore not retry
jfy133 Jul 17, 2020
05c25e2
Update main.nf
jfy133 Jul 20, 2020
6b9099f
Remove bedtools 137 ignore with bedtools less strict flag
jfy133 Jul 20, 2020
7fa167f
Update CHANGELOG.md
jfy133 Jul 20, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* [#497](https://github.com/nf-core/eager/issues/497) - Simplifies number of parameters required to run bam filtering
* [#501](https://github.com/nf-core/eager/issues/501) - Adds additional validation checks for MALT/MaltExtract database input files
* [#508](https://github.com/nf-core/eager/issues/508) - Made Markduplicates default dedupper due to narrower context specificity of dedup
* [#516](https://github.com/nf-core/eager/issues/516) - Made bedtools not report out of memory exit code when warning of inconsistant FASTA/Bed entry names

### `Dependencies`

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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -2026,8 +2026,8 @@ process bedtools {

script:
"""
bedtools coverage -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
bedtools coverage -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
"""
}

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