These are chat archives for nextflow-io/nextflow

17th
Sep 2018
Paolo Di Tommaso
@pditommaso
Sep 17 2018 09:33
you don't need MPI to run nextflow
Chris Fields
@cjfields
Sep 17 2018 14:55
Hi all, I'm looking for examples where one performs an additional optional step in between processes. In my particular case, I need to perform an additional (technology-specific) processing step after trimming and before alignment for some methylseq data: https://github.com/nf-core/methylseq/blob/93600734bc7a1c1a12a3848b4429425ee3aee79c/main.nf#L318
BTW, thanks @ewels and all for the amazing nf-core work!
Nothing useful in the patterns page?
Chris Fields
@cjfields
Sep 17 2018 15:02
Maybe the conditional + mix, but what I'm essentially trying to do is add a conditional step into a workflow with channels already in place.
Phil Ewels
@ewels
Sep 17 2018 15:04
Is the line you linked to not already a pattern that you can copy?
so - do an if/else block and if you're not doing the optional step you can create channels with the same name that your process would create in the output block
Alexander Peltzer
@apeltzer
Sep 17 2018 15:15
When directive could also work nicely here :smile:
Paolo Di Tommaso
@pditommaso
Sep 17 2018 15:15
exactly, here there's an example
then you can have the downstream process input defined with a condition
Chris Fields
@cjfields
Sep 17 2018 15:54
@pditommaso yes, I like the use of when in those examples. It does require changing the downstream process to accommodate the change but I think that would be needed regardless, and the input check seems cleaner
thx!
Paolo Di Tommaso
@pditommaso
Sep 17 2018 15:54
:v: