Mahmoud Ahmed

I am wondering if there is a way to control the content produced in the `multiqc` report when using the `--step` parameter. For example, when starting from recalibrated bam files,...

Why is the `ENSEMBLVEP_VEP` process not ran on chunks?

8

Hi there, I am trying to use sarek with `--step annotate --tools vep` with WGS vcf file as an input. The process `ENSEMBLVEP_VEP` takes too long because it attempts to...

Minor changes to stop complaining about zipped vcf files, as `vcfpy` already supports it ```console $ bcftools view test_data/out.ff.vcf -Oz -o test_data/out.ff.vcf.gz $ tabix test_data/out.ff.vcf.gz Apptainer> python3 src/stats --vcf test_data/out.ff.vcf.gz...

Running with `--single-mode True` produces the same error which was resolved #15 ```console Apptainer> jloh onco_extract --single-mode True --ref test_data/S_para.chrXII.fa --vcf test_data/out.ff.vcf --bam test_data/out.fs.bam [Thu Oct 2 11:40:06 2025] Initiating...

Runnin `jloh onco_extract` produces an error ```console Apptainer> jloh onco_extract --ref test_data/S_para.chrXII.fa --vcfs test_data/out.ff.vcf te st_data/out.ff.vcf --bams test_data/out.fs.bam test_data/out.fs.bam [Thu Oct 2 11:15:22 2025] Initiating onco_Jloh: checking conditions and organizing...