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Re-add pipe to ARFixPrefix to Pigz for speed #731

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Merged
jfy133 merged 5 commits into from
Apr 26, 2021
Merged

Re-add pipe to ARFixPrefix to Pigz for speed #731

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47e18a0
Update main.nf
jfy133 Apr 20, 2021
ad448fe
Update main.nf
jfy133 Apr 20, 2021
28ac4e4
Update CHANGELOG.md
jfy133 Apr 25, 2021
e612aad
Merge branch 'dev' into re-pipe-arfixprefix
jfy133 Apr 25, 2021
561ad8b
Merge branch 'dev' into re-pipe-arfixprefix
apeltzer Apr 26, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update
- Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow
- Updated DamageProfiler citation from bioRxiv to publication

### `Dependencies`
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24 changes: 6 additions & 18 deletions main.nf
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Expand Up @@ -791,9 +791,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz
"""
//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 @@ -807,9 +805,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz
"""
// 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 @@ -820,9 +816,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -835,9 +829,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -851,9 +843,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -867,9 +857,7 @@ 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 > output/${base}.pe.combined.fq

pigz -p ${task.cpus} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
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