Add optional trimming with Trim Galore

[chelauk]

nf-core/sarek pull request

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[maxulysse]

Hi @chelauk that looks like a very good start.

Could you add params to specify trimming options?

I think the rnaseq pipeline could be a good place to look at what to use already:
https://github.com/nf-core/rnaseq/blob/7c3aa75ec25db0d12a66181aed4fcbacf4b9901e/main.nf#L49-L57

Instead of --skipTrimming I would allow trimming only if said params are specified.
Do you think you could do that?

[chelauk]

I'm on to it.

[chelauk]

Could you add params to specify trimming options?

Yes

I think the rnaseq pipeline could be a good place to look at what to use already:
https://github.com/nf-core/rnaseq/blob/7c3aa75ec25db0d12a66181aed4fcbacf4b9901e/main.nf#L49-L57

Instead of --skipTrimming I would allow trimming only if said params are specified.
Do you think you could do that?

yes added --fastqTrim option

[maxulysse]

I just edited your comments for clarity

[chelauk]

when I use this command line I now get an error
nextflow run sarek -profile test,singularity --trim_fastq --clip_r1 2 --clip_r2 2

I am getting this error:

Caused by:
  Unknown variable 'clip_r1' -- Make sure it is not misspelt and defined somewhere in the script before using it

in nextflow.config it is defined:

params { 

 stuff = 'foo'
// options: Trimming
  trim_fastq = false
  clip_r1 = 0
  clip_r2 = 0
  three_prime_clip_r1 = 0
  three_prime_clip_r2 = 0
  trim_nextseq = 0
  skip_trimming = false
  save_trimmed = false

}

[chelauk]

nextflow run sarek -profile test,singularity --trim_fastq --clip_r1 2 --clip_r2 2 -with-singularity 'sifs/sarek.sif'
runs ok

[drpatelh]

Looks good @chelauk @maxulysse ! Couple of minor comments left. Ill approve so you can merge after fixing 👍

[chelauk]

sorry accidentally requested a review from @apeltzer

[maxulysse]

Looks perfect