David A. Parry

gatk/haplotypecaller requests huge java heap memory when run on SGE

1

**Snakemake version** snakemake: 6.13.0 wrapper: "v0.86.0/bio/gatk/haplotypecaller" **Describe the bug** When running gatk/haplotypecaller wrapper on an SGE cluster, a huge amount of java heap memory is requested. ``` rule call_variants: input:...

CanvasPedigreeCaller looking for hardcoded path to GenomeSize.xml

4

Hi, Using the precompiled release Canvas-1.38.0.1554+master_x64, I run into the following error when running the SmallPedigree-WGS workflow: ``` 2018-08-10T01:07:05+01:00,ERROR: Job CanvasPedigreeCaller failed with exit code 255. Job logs: /path/edited/for/privacy/canvas_cnv_calling/canvas_results/1268/Logging/CanvasPedigreeCaller.stdout /path/edited/for/privacy/canvas_cnv_calling/canvas_results/1268/Logging/CanvasPedigreeCaller.stderr...

Proposed change would allow script to run from any directory, sourcing leafcutter directory from the script location. Current code requires running of this script from a subdirectory of the leafcutter...