Port rnaseq subworkflows to nf-core/modules

[maxulysse]

Please convert each of this as an issue when you start working on one. (That can be done by clicking on the circle dot ⊙ at the end of the line in the list below, hover on a list item to see it) And label it with the appropriate pipeline label (ie :rnaseq). Note that a subworkflow can be useful for several pipelines.

• [x] #2264
• [x] #2180 rename to bam_sort_stats_samtools @KamilMaliszArdigen
• [x] new subworkflow bam_stats_samtools @drpatelh
• [x] #2194 rename to bedgraph_bedclip_bedgraphtobigwig @KamilMaliszArdigen
• [x] #2224 rename to bam_dedup_stats_samtools_umitools @KamilMaliszArdigen
• [x] #2253 @KamilMaliszArdigen
• [x] #2168 @dmarron
• [x] new subworkflow rseqc bam_rseqc @drpatelh

[pinin4fjords]

@maxulysse am I right in thinking that much of this is done now?

I'm a novice, but I'm seeing e.g. https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/bam_stats_samtools/main.nf already as of quite recently.

[SPPearce]

Is this all complete and the issue can be closed?