Jonathan Manning

As Evan mentioned on Slack, this does seem very verbose: ``` QUANTIFY_STAR_SALMON.out.results >> 'align' QUANTIFY_STAR_SALMON.out.tpm_gene >> 'align' QUANTIFY_STAR_SALMON.out.counts_gene >> 'align' QUANTIFY_STAR_SALMON.out.lengths_gene >> 'align' QUANTIFY_STAR_SALMON.out.counts_gene_length_scaled >> 'align' QUANTIFY_STAR_SALMON.out.counts_gene_scaled >> 'align' QUANTIFY_STAR_SALMON.out.tpm_transcript...

I'm loving the principle: ``` "${params.aligner}" { 'log' { from 'align-star-log' } from 'align-star-intermeds' 'unmapped' { from 'align-star-unaligned' } } ``` The multi import thing didn't occur to me. Could...

Really liking the way this is going now, it's going to be very tidy. Would it be feasible at some point to use some optional dynamism in the modules, to...

> Note that some subworkflows are now using params which is an anti-pattern. For this I recommend passing those params as workflow inputs to keep things modular. We have been...

This is now covered by the differential abundance workflow (which may need renaming at some point, since it does exploratory thing too). That workflow does indeed produce a markdown document...

@redvoidling I think I can see a possible solution here. In your local copy of the rnaseq workflow, could you try a fix for me? In [modules/nf-core/qualimap/rnaseq/main.nf](https://github.com/nf-core/rnaseq/blob/master/modules/nf-core/qualimap/rnaseq/main.nf), change: ``` export...

> Thank you! I will restart and get back to you on that. > > Another thought of mine would be to just run the Qualimap process in a loop...

That seems to have done the trick in removing the blocking error. My additional snippet just disabled some logging that probably isn't essential and seemed to be clashing. But it...

The log suggests to me that it's the writing of results that is taking time, which may be related to your local disks or other infrastructure. You can supply custom...

Glad it's working. Just be aware that changing the label changes more than just the time request, so you may for example be requesting more memory than you need.