new module: fgbio/fastqtobam about modules HOT 3 CLOSED

Following up with the discussion on jitsi:
Actually in the umitools dedup process, the read structure is passed via options.args rather than a val input, despite it being a mandatory argument.

https://github.com/nf-core/modules/blob/master/software/umitools/dedup/main.nf

from modules.

in terms of coding, doesn't make a big difference of course. But since the argument is mandatory, I believe it should have visibility and agree that options.args is more suitable for optional things. Just trying to put myself in another user's shoes, who is adding this module to their pipeline.

from modules.

As mentioned in the old PR, I've closed the PR and will start from scratch, in order to sync with latest template/master changes in nf-core.

from modules.