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

Skip to content

Fix post-ar trimming not being included in downstream analyses #823

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 9 commits into from
Jan 13, 2022
Merged

Fix post-ar trimming not being included in downstream analyses #823

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
005c150
Update main.nf
jfy133 Jan 11, 2022
b7fc2a4
Update CHANGELOG.md
jfy133 Jan 11, 2022
3dbee54
Update main.nf
jfy133 Jan 11, 2022
0e6d09c
Update CHANGELOG.md
jfy133 Jan 11, 2022
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
55f9afd
Merge pull request #825 from TCLamnidis/add_genome_to_bedtools
jfy133 Jan 12, 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
3 changes: 3 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `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`

### `Deprecated`
Expand Down
11 changes: 7 additions & 4 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1039,8 +1039,7 @@ if ( params.skip_collapse ){

// Inline barcode removal bypass when not running it
if (params.run_post_ar_trimming) {
ch_adapterremoval_for_skip_post_ar_trimming
.dump(tag: "inline_removal_bypass")
ch_post_ar_trimming_for_lanemerge
.into { ch_inlinebarcoderemoval_for_fastqc_after_clipping; ch_inlinebarcoderemoval_for_lanemerge; }
} else {
ch_adapterremoval_for_skip_post_ar_trimming
Expand Down Expand Up @@ -2055,8 +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
"""
}

Expand Down