oh no, so I think GATK and samtools are uncompatib...
# sarek_devr
Rike Hanssen
08/11/2026, 11:56 AMoh no, so I think GATK and samtools are uncompatible, not sure why the tests didn't flag this
m
Maxime Garcia
08/11/2026, 12:13 PMWHAT?
r
Rike Hanssen
08/11/2026, 12:13 PMI apparently got angry about this once already: https://nfcore.slack.com/archives/C043UU89KKQ/p1748935948486349
Rike Hanssen
08/11/2026, 12:14 PMinvestigating why the CI didn't flag this earlier
Rike Hanssen
08/11/2026, 12:30 PMthink I know why, ok this is a quick fix
m
Maxime Garcia
08/11/2026, 12:31 PMshakefist
r
Rike Hanssen
08/11/2026, 3:00 PMRike Hanssen
08/11/2026, 3:00 PMadded fix and a test for it + minor fix for parabricks container configs
Rike Hanssen
08/11/2026, 3:01 PMquiet possible that the snapshots need updating
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