<@U0938586SPK> So let's keep the QC Subworkflow on...
# sarek_devm
Maxime Garcia
06/26/2026, 10:16 AM@Agrima Bhatt So let's keep the QC Subworkflow on the side for now, I will continue to write down ideas there.
I think you can start on:
• bam_applybqsr
• bam_baserecalibrator
• bam_markduplicates
@Rike Hanssen regarding that, do we want to keep spark or not?
👍 1
Maxime Garcia
06/26/2026, 10:19 AMI do think the input for these subworkflow can be further simplified, if we rewrite the input to be:
cram, intervals, references
we might need to touch the underlying modules for that
Maxime Garcia
06/26/2026, 10:25 AMI do think we can try to ditch the bam_merge_index_samtools and cram_merge_index_samtools, and just replace with samtools_merge with -write-index
r
Rike Hanssen
06/26/2026, 10:32 AMdidn't we do this already?
m
Maxime Garcia
06/26/2026, 10:37 AMMaxime Garcia
06/26/2026, 10:37 AMDo we want to keep spark?
r
Rike Hanssen
06/26/2026, 10:37 AMhm must have been in a different pipeline
m
Maxime Garcia
06/26/2026, 10:37 AMIf so, maybe we could merge the spark and non spark subworkflows
m
Matthias De Smet
06/26/2026, 10:54 AMHot take, are the spark workflows actually used by somewhere? Because those modules are the flakiest I’ve ever seen
m
Maxime Garcia
06/26/2026, 10:55 AMok, so let's drop support for it in sarek then?
r
Rike Hanssen
06/26/2026, 11:17 AMIf so, maybe we could merge the spark and non spark subworkflowsno, because they need slightly different upstream processing
👍 1
Rike Hanssen
06/26/2026, 11:17 AMHot take, are the spark workflows actually used by somewhere? Because those modules are the flakiest I’ve ever seenunsure we have had a few bug reports soooooo maybe?
m
Maxime Garcia
06/26/2026, 11:18 AM😐
m
Matthias De Smet
06/26/2026, 11:18 AMthe spark stuff is a PITA to update in #CJRH30T6V
r
Rike Hanssen
06/26/2026, 11:29 AMmaybe we can deprecate it and just not update it anymore and print a warning? If people start complaining we know someone is using it?
3 Views