search

nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
195 stars 150 forks source link

cutadapt `trim_nextseq` config typo #429

Closed cmatKhan closed 1 month ago

cmatKhan commented 1 month ago

The parameter documentation

https://github.com/nf-core/chipseq/blob/76e2382b6d443db4dc2396e6831d1243256d80b0/nextflow_schema.json#L210

and the cutadapt docs

https://cutadapt.readthedocs.io/en/stable/guide.html#nextseq-trim

seem to say that the cutadapt parameter is nextseq-trim. But the conf file sets it to just nextseq

https://github.com/nf-core/chipseq/blob/76e2382b6d443db4dc2396e6831d1243256d80b0/conf/modules.config#L138C50-L138C57

I think that should read:

params.trim_nextseq > 0 ? "--nextseq-trim ${params.trim_nextseq}" : '',

rather than

params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '',
cmatKhan commented 1 month ago

edit -- nextseq is the correct trimgalore setting. my bad