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Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore … #845

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Merged
jfy133 merged 2 commits into from
Mar 17, 2022
Merged

Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore … #845

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9481c84
Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore …
jfy133 Mar 10, 2022
01a89a0
Merge branch 'dev' into arfp-pigz-fix
jfy133 Mar 17, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`

- [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz

### `Dependencies`

### `Deprecated`
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20 changes: 8 additions & 12 deletions main.nf
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Expand Up @@ -811,8 +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 > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${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 @@ -826,8 +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 > output/${base}.pe.combined.fq
pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${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 @@ -838,8 +838,7 @@ 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 ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -852,8 +851,7 @@ 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 ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -867,8 +865,7 @@ 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 ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
Expand All @@ -882,8 +879,7 @@ 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 ${task.cpus - 1} output/${base}.pe.combined.fq
AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz

mv *.settings output/
"""
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