Ascat computes all possible N-T combinations

[ggabernet]

Hi, I was wondering why 25 ascat processes were started when I had just 5 Tumor-Normal pairs, and it turns out that ascat computes all possible N-T combinations. Eg:

Ascat_CHC2113T_vs_CHC2113N
Ascat_CHC2113T_vs_CHC2115N
Ascat_CHC2113T_vs_CHC912N

I can also help with fixing that, just wanted to document it in an issue :)

[lconde-ucl]

We fixed it in our local copy of sarek by adding by: 0 in alleleCountNormal.combine. Please note that alleleCountOutput.map needs to be modified accordingly too:

alleleCountOutput
  .choice(alleleCountTumor, alleleCountNormal) {it[1] == 0 ? 1 : 0}

alleleCountOutput = alleleCountNormal.combine(alleleCountTumor, by: 0)

alleleCountOutput = alleleCountOutput.map {
  idPatientNormal, statusNormal, idSampleNormal, alleleCountNormal,
  statusTumor,  idSampleTumor,  alleleCountTumor ->
  [idPatientNormal, idSampleNormal, idSampleTumor, alleleCountNormal, alleleCountTumor]
}

Hope this helps
Lucia

PS: I should have specified that the above changes fixed this issue in the "SciLifeLab/Sarek" pipeline, which is the pipeline we were using, but the same changes should fix it in "nf-core/sarek" as well