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

Remove old fastq.STATUS.tsv files #144

Open
LennertVerboven opened this issue Feb 20, 2023 · 0 comments
Open

Remove old fastq.STATUS.tsv files #144

LennertVerboven opened this issue Feb 20, 2023 · 0 comments

Comments

@LennertVerboven
Copy link
Collaborator

In the fastq_validator script we need to remove previously existing fastq.STATUS.tsv files. Now if you run the pipeline and one samples fails fastq_validator and ends up in the fastq.failed.tsv it will remain there forever. When you fix the fastq files and rerun the pipeline with -resume, the old fastq.failed.tsv file does not get overwritten or deleted in the publish directory, and will now show up in both the fastq.failed.tsv and fastq.passed.tsv files

echo -e "!{sampleName}\t${VALIDATED}" > !{sampleName}.check.${STATUS}.tsv

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

No branches or pull requests

1 participant