Skip to content

Kraken2 empty fastq resulting in no output file fix #898

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 5 commits into from
Jul 8, 2022
Merged

Kraken2 empty fastq resulting in no output file fix #898

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
204ca23
Allow no output from Kraken2 e.g. for negative controls with no reads
jfy133 Jul 1, 2022
898b643
Update CHANGELOG.md
jfy133 Jul 1, 2022
99053b5
Merge branch 'dev' into kraken2-emptyfastq-fix
jfy133 Jul 4, 2022
634ae16
Merge branch 'dev' into kraken2-emptyfastq-fix
jfy133 Jul 4, 2022
881e85f
Update output.md
jfy133 Jul 8, 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 @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
- [897](https://github.com/nf-core/eager/issues/897) Fix pipeline crashing if no Kraken2 results generated (♥ to @alexandregilardet for reporting)

### `Dependencies`

Expand Down
4 changes: 2 additions & 2 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3019,8 +3019,8 @@ process kraken {
path(krakendb) from ch_krakendb

output:
file "*.kraken.out" into ch_kraken_out
tuple prefix, path("*.kraken2_report") into ch_kraken_report, ch_kraken_for_multiqc
file "*.kraken.out" optional true into ch_kraken_out
tuple prefix, path("*.kraken2_report") optional true into ch_kraken_report, ch_kraken_for_multiqc

script:
prefix = fastq.baseName
Expand Down
⚡