Thanks to visit codestin.com
Credit goes to github.com

Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
- [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
- [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
- Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask
Expand Down
20 changes: 8 additions & 12 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -823,8 +823,8 @@ 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 @@ -838,8 +838,8 @@ 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 @@ -850,8 +850,7 @@ 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 @@ -864,8 +863,7 @@ 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 @@ -879,8 +877,7 @@ 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 @@ -894,8 +891,7 @@ 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 Down