Jakob Willforss
Jakob Willforss
### Description of the bug In `GATK4_POSTPROCESSGERMLINECNVCALLS`, the memory is handled in megabytes, but assigned to the java process in gigabytes. See: https://github.com/nf-core/raredisease/blob/master/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf If for instance having access to 20GB,...
This is something we are looking at over at the https://github.com/Clinical-Genomics/chanjo2 repo. The current approach is to read the output from the d4 file using `d4tools show`. It would be...
Leaving this for reference. Working with #78, I also tried running indexed d4 files. Here, I also got strange results. I traced it in the code, and did not seem...
### Description of the bug The crash: ``` ERROR ~ Cannot invoke method collectEntries() on null object -- Check script './workflows/../subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 110 or see '.nextflow.log' file for more...
### Description of the bug The Sentieon DNAScope takes a flag `--model` which is expected to point to a file with a pre-trained model. In their latest updates, the models...
Hello, and thanks for this cool pipeline! I have been spending some time debugging DROP. The last error was for the aberrant expression workflow inside the `Summary.R` script from the...
We found this when working with long reads data, where coverage bins tend to be longer than for short reads data. We use d4tools to calculate bin-by-bin coverage. Here, frequently,...
Trying to prepare a unit test dataset for #113 on a moderately small bedgraph dataset (580 intervals), ended up processing for many hours before I cancelled the job. Seems something...