Skip to content
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.

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

Do not run RSeQC tin.py by default #769

Closed
drpatelh opened this issue Feb 20, 2022 · 1 comment
Closed

Do not run RSeQC tin.py by default #769

drpatelh opened this issue Feb 20, 2022 · 1 comment
Labels
enhancement WIP Work in progress
Milestone

Comments

@drpatelh
Copy link
Member

Description of feature

A number of users have reported that the RSeQC tin.py module added in v3.4 is causing issues - mainly due to very long run-times. By default, the module has a label of process_medium which means it runs for 8 hours but is still failing. I don't think it makes sense to have such a long running QC step on by default in the pipeline and as such it should be opt-in rather than set by default.

Once it has been removed you can run tin.py by appending tin to the --rseqc_modules parameter like below:

--rseqc_modules 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication,tin'

@drpatelh drpatelh added this to the 3.6 milestone Feb 20, 2022
@drpatelh drpatelh added the WIP Work in progress label Feb 20, 2022
drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue Feb 21, 2022
@drpatelh
Copy link
Member Author

Process label bumped to process_high in nf-core/modules#1327, re-installed in the pipeline and made opt-in in #771

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement WIP Work in progress
Projects
None yet
Development

No branches or pull requests

1 participant