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

Changes in sample_info 'stranded' field to not trigger rerun of STAR mapping #27

Open
Nicolai-vKuegelgen opened this issue Sep 20, 2023 · 0 comments · May be fixed by #28
Open

Changes in sample_info 'stranded' field to not trigger rerun of STAR mapping #27

Nicolai-vKuegelgen opened this issue Sep 20, 2023 · 0 comments · May be fixed by #28

Comments

@Nicolai-vKuegelgen
Copy link

Sometimes one wants/needs to change the information in the 'stranded' field of the sample_info.yaml file, i.e. if information was wrong or not available before the first run. A change in this parameter should trigger a rerun of STAR and all downstream rules. However, this does currently not happen.

Proposed solution: with the newerst snakemake version a rerun can be triggered by changes in the rule params. Therefore adding the following line (adapted form from the run block) to the params section in the STAR rule should fix this issue:
count_col = lambda wildcards: {"unstranded":2, "forward":3, "reverse":4}[config["sample_info"][wildcards.sample]["stranded"]]

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

Successfully merging a pull request may close this issue.

1 participant