Simon Pearce
Simon Pearce
Ok, thanks. Yes, anything that can be a file input must be staged via the input channels, as Nextflow expects all its inputs to be inside the work directory. On...
Also I note that one of the arguments is called seed. If that is controlling randomness, does the default produce reproducible results? If not, then I'd be keen for that...
@sguizard , are you able to finish this PR off and get these changes merged in? Please ask if you need help. Conda often gives md5sums for bam files that...
I was curious as to why the versions.yml was changing, so I took the output of `pbmerge --version` in the two containers: conda: ``` "PBBAM_PBMERGE": pbbam: pbmerge 3.1.1 (commit v3.1.1)...
> Second comment: It seems to me that [pbbam was archived](https://github.com/PacificBiosciences/pbbam) and the individual tools were transferred to [pbtk](https://github.com/PacificBiosciences/pbtk). I think this should be reflected in the nf-core modules? >...
As discussed on the slack channel, I would suggest that we leave the pbmerge module untouched in this PR, and open a separate PR to deprecate it (rather than delete...
Good work @sguizard 🎉
Oh, this is pytest still? Can we swap to nf-test?
@mribeirodantas , is this ready for review?
@mribeirodantas ?