@Ata Jadid Ahari could you finish your review of this PR? https://github.com/nf-core/drop/pull/94 This one is holding up the release 😛

I just approved this.

Awesome! I'll go through all the PRs now and setup a release PR

Thanks!

There still seem to be some issues in the R scripts... do you have time to take a look at it? (Just running the test profile fails). I could also do it but I'm not that familiar with the scripts 😛

I will check this later today.

Thanks! Let me know if I can help with something

It seems like the external are causing the problem. somewhere around here which is not in the snakemake version so not sure what is happening: https://github.com/nf-core/drop/blob/update/strict-syntax/modules/local/genecounts/summary/templates/Summary.R#L44

That line is in the snakemake version: https://github.com/gagneurlab/drop/blob/90fa2b6a43e03f5cd124c1b734be15bede1385dc/drop/modules/aberrant-expression-pipeline/Counting/Summary.R#L52

I did a bit of debugging, and found two problems: • in filtercounts, the

== ""

is not enough, and the isExternal was NA for local samples. This was causing the problem you saw in your branch @Nicolas Vannieuwkerke. • in countreads,

colnames(se) <- "{$meta.id}"

now assigns incorrect names to the samples. It puts the brackets too, i.e.

{sample_id}

instead of

sample_id

. maybe this is an artifact of the latest renaming pr? I made some changes and pushed now. Hope it fixes the issue.

Awesome! I'll see if this fixes my issues 🙂

That error is fixed now. But we are getting different snapshots for splicing module now. I wonder what changed for this to happen.

It was a connection issue, I've restarted the test 🙂

Yes go ahead and merge. Thanks!

Done, thanks!