Harshil Patel

Thanks @apeltzer! I was thinking it would be nice if we could maybe automatically add the list of available profiles to the help string produced by the pipeline. Maybe we...

> But is the idea to resolve against the work directory only in specific cases, like if the executor is awsbatch or the launch directory is / or a nextflow...

It would be nice to have a config option for this as well as an env setting. Or would you suggest using something like this instead @pditommaso? ```nextflow env {...

Hi @FlorianRNA ! As stated in the [usage docs](https://nf-co.re/rnaseq/3.8.1/usage#quantification-options) for the nf-core/rnaseq pipeline: "Since v3.0 of the pipeline, featureCounts is no longer used to perform gene/transcript quantification, however it is...

Ah, my bad. I assumed you were running featureCounts via the pipeline. Thanks for clarifying. Happy to incorporate changes into the pipeline in the future if they improve the default...

Thanks! This won't work when we need to use a closure with `collect` though like below: https://github.com/nf-core/rnaseq/blob/e049f51f0214b2aef7624b9dd496a404a7c34d14/workflows/rnaseq.nf#L777-L786 Given that we will have to use a closure to remove the `meta`...

Hi @mimifp ! Are you able to send the `.nextflow.log` files for the runs before and after you used all of the skip steps? There should also be some files...

Agree we should maybe have an option to switch the stats off. Still think we should keep it in the name though otherwise what distinguishes it from another subworkflow that...

Somewhat a duplicate of https://github.com/nf-core/fetchngs/issues/111

Fixed in https://github.com/nf-core/fetchngs/pull/115/commits/d67b3ef6eaf437c7a22da800fcb0d26f19d0a9a7