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
Add bam filtering on fragment length script #544
Conversation
Nice 👍 |
Doesn't add the script to the nextflow code no? We need to test this ;-) |
That's the plan, don't worry! |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Only issue I can see is that: during testing, -a
seems to do nothing.
(samtools) sos@dat4903339:10:28:bwa:(dev)$ samtools stats filtered_py_ohneA.filtered.bam | grep ^FRL | cut -f 2- | head
31 2
32 2
33 2
34 4
35 1
36 4
37 4
38 5
39 4
40 8
(samtools) sos@dat4903339:10:28:bwa:(dev)$ samtools stats filtered_py_withA.filtered.bam | grep ^FRL | cut -f 2- | head
31 2
32 2
33 2
34 4
35 1
36 4
37 4
38 5
39 4
40 8
This should now include unmapped reads https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignmentFile.fetch |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Works for me now, thanks @maxibor! Will merge and make a new PR to replace the awk, and hopefully this makes CI more stable 💪
Add bam filtering on fragment length script
PR checklist
nextflow run . -profile test,docker --paired_end
).nf-core lint .
).docs
is updatedCHANGELOG.md
is updatedREADME.md
is updatedLearn more about contributing: CONTRIBUTING.md