search

SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
133 stars 7 forks source link

Copy results even if Ascat fails #289

Closed malinlarsson closed 6 years ago

malinlarsson commented 7 years ago

In some cases ASCAT fails to create a model for tumor purity and average ploidy. I have seen this in one case so far, but it is known that it happens for a certain fraction of tumors that are particularly complicated to assess. In such cases it would be good if part of the output from "runAscat" is still copied to the VariantCalling/Ascat folder. For example, the plots of raw data (xxx.tumor.png) and segmented data (xxx.ASPCF.png). This is useful information, especially together with a note that "ascat failed to find an estimation of average ploidy and purity").

maxulysse commented 7 years ago

Do you think it could be fixed by getting all files in the output channel, using file("${idSampleTumor}.*.png"), file("${idSampleTumor}.*.txt") ?

maxulysse commented 6 years ago

Copy results even if Ascat fails

maxulysse commented 6 years ago

We will reopen it if needed.