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Adapterremovalfixprefix sep #793

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Merged
jfy133 merged 1 commit into from
Sep 14, 2021
Merged

Adapterremovalfixprefix sep #793

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#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
- [#792](https://github.com/nf-core/eager/issues/792) Fixed java error messages for AdapterRemovalFixPrefix being hidden in output

### `Dependencies`

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18 changes: 12 additions & 6 deletions main.nf
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Expand Up @@ -811,7 +811,8 @@ process adapter_removal {
mv *.settings output/

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
"""
//PE mode, collapse and trim, outputting all reads, preserving 5p
} else if (seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && !params.mergedonly && params.preserve5p) {
Expand All @@ -825,7 +826,8 @@ process adapter_removal {
mv *.settings output/

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
"""
// PE mode, collapse and trim but only output collapsed reads
} else if ( seqtype == 'PE' && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) {
Expand All @@ -836,7 +838,8 @@ process adapter_removal {
cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq

mv *.settings output/
"""
Expand All @@ -849,7 +852,8 @@ process adapter_removal {
cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq

mv *.settings output/
"""
Expand All @@ -863,7 +867,8 @@ process adapter_removal {
cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq

mv *.settings output/
"""
Expand All @@ -877,7 +882,8 @@ process adapter_removal {
cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz

## Add R_ and L_ for unmerged reads for DeDup compatibility
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq

mv *.settings output/
"""
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