Maxime U Garcia
Maxime U Garcia
ok, so `picard` should be patched as well, I'll do that in a separate PR then...
Changed the name of the issue and kept it open, so that we can track other JAVA tools. all gatk4 modules have been patched (cf #3844), and we have a...
Realizing that the issue is most likely due to the fact that when one modify `testDir` to `.` to include all tests as we would do in nf-core, then `.`...
pytests issues should be fixed when we migrate
Good catch up on this PR @famosab
> @nf-core/core do we need special tokens or keys on the modules repo to be available to access S3 stuff? What do you need?
I'm on tiddit and manta
I'd say you need to adapt https://github.com/nf-core/sarek/blob/dev/subworkflows/local/fastq_preprocess_gatk/main.nf#L166 as well. Or else, add this field to the meta map in https://github.com/nf-core/sarek/blob/dev/subworkflows/local/fastq_preprocess_parabricks/main.nf only
Nice. Can you add mutect2 to the test
Let's update the tests to the new syntax, and merge this