bedtools warning

[yassineS]

Bedtools occasionally issues a warning like this when using GRCh38:

***** WARNING: File merged_bams/initial/A14937_libmerged_rg_rmdup.bam has inconsistent naming convention for record:
HLA-A*01:01:01:01	47	100	M_ST-E00180:295:H7JNVCCXY:7:2220:15229:45699	0	+

Bedtools continues running and produces a complete output. However, the error 137 results in the process being identified as "failed" by nextflow. It just requires an exception.

[jfy133]

Thanks for the report @yassineS !

Could you maybe run a manual test, and see if the following solution works?

arq5x/bedtools2#628 (-noname)

If so I would prefer for that to work than 'ignoring' the error code, but in case it doesn't work, please can you test the fix on this branch: https://github.com/nf-core/eager/tree/bedtools-fix/

[yassineS]

Thanks, @jfy133 Just for the record, there are no mismatches between chromosome names in the bed file, the reference and the bam file.

I tried the -nonamecheck option and it seems to have fixed the issue.

[jfy133]

Should be addressed inthe above!