Skip to content

Add Skipping FastQC #186

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
apeltzer merged 4 commits into from
Apr 9, 2019
Merged

Add Skipping FastQC #186

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
af2abfa
Add changelog
apeltzer Apr 8, 2019
74127bf
Add changelog pull reference
apeltzer Apr 8, 2019
087884e
Add user docs
apeltzer Apr 8, 2019
02b7748
This should do :-)
apeltzer Apr 8, 2019
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
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Added`

* [#186](https://github.com/nf-core/eager/pull/186) - Make FastQC skipping [possible]
/(https://github.com/nf-core/eager/issues/182)
### `Fixed`
* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)

Expand Down
4 changes: 4 additions & 0 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -299,6 +299,10 @@ Turns off the computation of library complexity estimation.

Turns off adaptor trimming and paired-end read merging. Equivalent to setting both `--skip_collapse` and `--skip_trim`.

### `--skip_fastqc`

Turns off FastQC in the beginning to speed up the pipeline.

### `--skip_damage_calculation`

Turns off the DamageProfiler module to compute DNA damage profiles.
Expand Down
5 changes: 4 additions & 1 deletion main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,7 @@ params.email = false
params.plaintext_email = false

// Skipping parts of the pipeline for impatient users
params.skip_fastqc = false
params.skip_adapterremoval = false
params.skip_preseq = false
params.skip_damage_calculation = false
Expand Down Expand Up @@ -532,6 +533,8 @@ process fastqc {
publishDir "${params.outdir}/FastQC", mode: 'copy',
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}

when: !params.skip_fastqc

input:
set val(name), file(reads) from ch_read_files_fastqc.mix(ch_read_files_converted_fastqc)

Expand Down Expand Up @@ -650,7 +653,7 @@ process fastqc_after_clipping {
publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}

when: !params.bam && !params.skip_adapterremoval
when: !params.bam && !params.skip_adapterremoval && !params.skip_fastqc

input:
set val(name), file(reads) from ch_clipped_reads_for_fastqc
Expand Down
⚡