Add bam filtering on fragment length script

[maxibor]

Add bam filtering on fragment length script

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
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• Make sure your code lints (nf-core lint .).
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[jfy133]

Thanks @maxibor ! @apeltzer this is hopefully to replace the shaky awk hack I have... will look next week.

[drpatelh]

Nice 👍

[apeltzer]

Doesn't add the script to the nextflow code no? We need to test this ;-)

[jfy133]

Doesn't add the script to the nextflow code no? We need to test this ;-)

That's the plan, don't worry!

[jfy133]

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

[maxibor]

This should now include unmapped reads https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignmentFile.fetch

[jfy133]

Works for me now, thanks @maxibor! Will merge and make a new PR to replace the awk, and hopefully this makes CI more stable 💪