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.

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

Jump to bottom

error when coverage is null for every bam file #99

Closed
tdelhomme opened this issue Apr 7, 2016 · 0 comments
Closed

error when coverage is null for every bam file #99

tdelhomme opened this issue Apr 7, 2016 · 0 comments
Assignees
@tdelhomme
Labels
bug
Milestone
v0.3

Comments

@tdelhomme
Copy link
Member

If we try to call a region where the coverage is null for every files, samtools_mpileup will produce an empty file and mpileup2table will not output any sample*.txt whereas they are required outputs.

Error running process > Missing output file(s): 'sample*.txt' expected by process: mpileup2table

We have to stop the pipeline after samtools_mpileup process if all emitted mpileup files are empty.
@tdelhomme tdelhomme added this to the v0.3 milestone Apr 7, 2016
@tdelhomme tdelhomme self-assigned this Apr 7, 2016
tdelhomme referenced this issue Apr 7, 2016
@tdelhomme
no output vcf if mpileup produces an empty file
e7da6fb 
We manage the case when `samtools_mpileup` produces an empty file.
This appears when the coverage is null for all calling regions.
Before, in this case the pipeline crashed (no needed output `sample*.txt` from `pileup2table`).
@mfoll mfoll added the bug label Apr 25, 2016
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@tdelhomme tdelhomme

Labels
bug
Projects
None yet
Milestone
v0.3
Development

No branches or pull requests
2 participants
@mfoll @tdelhomme