Migrate local modules to nf-core/modules

[apeltzer]

Description of feature

Wherever possible (e.g. BLAT), this should be performed. Prime candidates for this are:

• BLAT
• edgeR
• mirDeep2
• mirtop
• mirtrace
• seqcluster
• bowtie1/bowtie2 modules (~5 of them)

Tasks

Beta Give feedback

1. Migrate local BLAT to nf-core modules #395
   +0
   
2. Create nf-core mirTrace module #402
   +0
   
3. Add nf-core mirTrace module to smrnaseq #410
   +0
   
4. Create nf-core mirtop module #403
   +0
   
5. Add nf-core mirtop module to smrnaseq #417
   +0
   
6. Create nf-core seqcluster module #413
   +0
   
7. Add nf-core seqcluster to smrnaseq #416
   +0
   
8. Replace custom code with nf-core/modules/pigz/uncompress #422
   bug +1
   
9. Create nf-core mirdeep module #431
   +0
   
10. Add nf-core bowtie1 build to smrnaseq #433
    +0
    
11. Add nf-core bowtie2 build to smrnaseq #434
    +0
    
12. Add nf-core bowtie align to smrnaseq #436
    +0
    
13. Update mirtop to latest version #437
    +0
    
14. Add nf-core mirdeep to smrnaseq #443
    +0
    

[apeltzer]

I will check this one if we really want to overinvest on this ticket here - I think the progress is already great 👍🏻

[apeltzer]

Lets not do EdgeR, its quite specific to smrnaseq.

MirTop lets report upstream / file an issue and just do the very same as before but in nf-core/modules @atrigila