RSEQC3.0 Support

[apeltzer]

No description provided.

[apeltzer]

Seams updating to the 3.0.0 recipe doesn't break anything locally, which is a good start 👍

#148

I'll make the changes to utilize the former way of doing things without the bigWig later.

[apeltzer]

MultiQC Report looks sane to me as well:

multiqc_report.html.zip

[apeltzer]

Looks ok to me @ewels what do you think?

multiqc_report.html.zip

This is on RSEQC3.0, with subsampling again without actually creating bigWig files anymore. Runtime was

The workflow was completed at Thu Jan 31 16:39:35 CET 2019 (duration: 3m 46s)

The command used to launch the workflow was as follows:

[ewels]

Looks great! To be honest, I can't remember which rseqc outputs generated MultiQC sections before. But good that gene body coverage is still there 👍

[ewels]

Looks great! Couple of minor suggestions.

Separate note: it would be good to cut the .sorted.markDups off the sample names for MultiQC. Needs a minor addition to multiqc_config.yml:

extra_fn_clean_exts:
    - '.sorted.markDups'

(also, it's confusing as hell that the test input files have _subsamp.fastq.gz filenames 😆 - maybe we should rename them for clarity?)

[apeltzer]

I think this is fine to go ...?

[ewels]

Nearly! Couple of minor docs suggestions. I was also looking for it to be added to nextflow.config but now I realise what you mean - that it's already there from a previous iteration. Looking good! 👍

[ewels]

Brilliant stuff - thanks!