Update to topic qualimap

[LouisLeNezet]

PR checklist

Closes #12622

• This comment contains a description of changes (with reason).
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[SPPearce]

I don't really like breaking the existing code like this, by just ignoring the strandedness entirely.

[LouisLeNezet]

My reasoning is that it is an optional argument for these tools (non-strand-specific as default).
As such, shouldn't it be passed through ext.args ?

[SPPearce]

Yeah, in theory ;)
Personally I think meta.strandedness should still be allowed

[LouisLeNezet]

Okay, I will put it back then !

[SPPearce]

Well, it isn't allowed by the linter at the moment

[LouisLeNezet]

Yeah, now I remember why I deleted it 😕
What's the recommended course of action ?
Should we move it to a separate value channel ?

[LouisLeNezet]

Hi @SPPearce,

Should I go for something like:

withName:PICARD_COLLECTRNASEQMETRICS {
    ext.args = {
        ( meta.strandedness == "forward" || meta.single_end ) ?
        "--STRAND_SPECIFICITY FIRST_READ_TRANSCRIPTION_STRAND" :
        meta.strandedness == "reverse" ?
        "--STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND" :
        "--STRAND_SPECIFICITY NONE"
    }
}