Hi all, I'm struggling a bit updating

Bamcmp

that uses:

def prefix = task.ext.prefix
def prefix2 = task.ext.prefix2

linting did not complain with nf-core tools 3.5.2 but with version 3.6.0.dev0 (run in CI) and breaks my PR (#11199). Do we allow only one

ext.prefix

these days? Not sure about the strategy on how to resolve it. shall I just swap

prefix2

to a unused

args

and document it accordingly?

Already went through it. In the module it’s hitting an edge case, I think prefix2 is used as a fall back

Uhhh

I have it as ‚ext.args3‘ now

ugh that is gross

Do the prefixes need to be that flexible? Can one not use

bamcmp \\
        -1 $primary_aligned_bam \\
        -2 $contaminant_aligned_bam \\
        -A ${prefix}_primary.sam \\
        -B ${prefix}_contaminant.sam \\
        $args

?

Sure, you could. In my previous place we used "human" and "mouse", because that was what they were

Yes, tests ran fine with prefix2 but linting breaks.

For nf-core modules, I would suggest a single prefix, but when you include in your pipeline, you can modify how you want and use

nf-core modules patch

to save the modifications when updates need to be included. If there enough use case for

prefix2

then I guess one needs to make a proposal.