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

Error when running PCAWG pipeline #27

Open
ashraf123456789 opened this issue Aug 9, 2023 · 0 comments
Open

Error when running PCAWG pipeline #27

ashraf123456789 opened this issue Aug 9, 2023 · 0 comments

Comments

@ashraf123456789
Copy link

Hello,

when I run the command : dockstore tool launch --entry --script quay.io/pancancer/pcawg-bwa-mem-workflow:2.7.0 --json Dockstore_cwl.json.txt

This downloads all the files in the github repository to the datastore directory, but doesn't run the alignment pipeline afterwards, citing that the bam.bai's are not present in a merging step.

ERROR [job Seqware-BWA-Workflow] Job error:
("Error collecting output for parameter 'merged_output_bai': ../../../tmp/1691622356648-0/Dockstore.cwl:94:7: Did not find output file with glob pattern: '['datastore/hg19.chr22.5x.normal.bam.bai']'.", {})

There's no bam.bai's present in the current repository. I'm not sure if the pipeline is supposed to generate this. Plase let me know if you can assist with this.
dockstore_launch.log

Best,
-Ashraf

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