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Merge pull request #518 from nf-core/bedtools-fix
Bedtools fix
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CHANGELOG.md

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@@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
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* [#497](https://github.com/nf-core/eager/issues/497) - Simplifies number of parameters required to run bam filtering
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* [#501](https://github.com/nf-core/eager/issues/501) - Adds additional validation checks for MALT/MaltExtract database input files
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* [#508](https://github.com/nf-core/eager/issues/508) - Made Markduplicates default dedupper due to narrower context specificity of dedup
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* [#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
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### `Dependencies`
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main.nf

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@@ -2026,8 +2026,8 @@ process bedtools {
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script:
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"""
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bedtools coverage -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
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bedtools coverage -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
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bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
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bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
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"""
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}
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