Add read group back and crumble for HiFi

[priyanka-surana]

No description provided.

[muffato]

Is there a small PacBio file we could use in the test profile ? Had to run the full test profile to see the outcome of this change.

Shane also suggested to add the -c and -p options to samtools merge in order to remove redundant @RG (and @PG) headers. Could you add that ?

[priyanka-surana]

Is there a small PacBio file we could use in the test profile ? Had to run the full test profile to see the outcome of this change.

The PacBio sample in the test_full is one of the smallest. The only way I know to subset a PacBio BAM is to convert to a regular BAM. We can look into that more.

Shane also suggested to add the -c and -p options to samtools merge in order to remove redundant @RG (and @PG) headers. Could you add that ?

Done ✅

[priyanka-surana]

I updated the docker.registry which led to updating lots of modules. It is in prep for template update.

[muffato]

My "full_test" run stopped because of a RUNLIMIT / exit code 140 on SANGERTOL_READMAPPING:READMAPPING:ALIGN_ONT:MINIMAP2_ALIGN (ilPolIcar4_T1).
errorStrategy in conf/base.config indeed doesn't contain the 140. Could you add that ? or make it match the nf-core template ? (which now has a range)

[priyanka-surana]

My "full_test" run stopped because of a RUNLIMIT / exit code 140 on SANGERTOL_READMAPPING:READMAPPING:ALIGN_ONT:MINIMAP2_ALIGN (ilPolIcar4_T1).
errorStrategy in conf/base.config indeed doesn't contain the 140. Could you add that ? or make it match the nf-core template ? (which now has a range)

This might be because of the change in sanger.config because with the old version we had a default retry strategy. I have made the update, but will push later, since I was in the middle of some other changes too.

[muffato]

Approving as I have no concerns about the code, and it's been used in production for a few months !