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Bedtools process changes #825

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Merged
jfy133 merged 4 commits into from
Jan 12, 2022
Merged

Bedtools process changes #825

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789c12e
bedtools: Add genome and sorted flags
TCLamnidis Jan 12, 2022
180b6a7
avoid slashes in sed, escape backslash
TCLamnidis Jan 12, 2022
3929b58
Fixed bedtools memory needs
TCLamnidis Jan 12, 2022
b9622a3
Update CHANGELOG.md
jfy133 Jan 12, 2022
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Added`

### `Fixed`

- [#824](https://github.com/nf-core/eager/issues/824) Fixes large memory footprint of bedtools coverage calculation.
- [#822](https://github.com/nf-core/eager/issues/822) Fixed post-adapterremoval trimmed files not being lane-merged and included in downstream analyses

### `Dependencies`
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8 changes: 6 additions & 2 deletions main.nf
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Expand Up @@ -2054,8 +2054,12 @@ process bedtools {

script:
"""
bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
## Create genome file from bam header
samtools view -H ${bam} | grep '@SQ' | sed 's#@SQ\tSN:\\|LN:##g' > genome.txt

## Run bedtools
bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
"""
}

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