mskilab-org / nf-jabba Goto Github PK

Description of the bug

Dear maintainer,

Thanks for creating this pipeline! I would like to run it on some BAM files to get JaBbA CNV calls. I managed to run the SV calling by SVABA, but the pipeline said that it was completed after the SV calling when ascat and JaBbA were not run.

These are the result directories that I currently have:

Coverages Hetpileups msisensorpro pipeline_info SV_calling tabix

The Coverages/Dryclean_normal/ and Coverages/Dryclean_tumor/ have subdirectories for each sample, but these directories are empty. Could this be the issue?

Meanwhile, may I please confirm that I need to manually add CPLEX to the Docker container, so to create my own container for running the pipeline?

Thank you for your help!

Kind regards,
Yuyao

Command used and terminal output

nextflow run mskilab-org/nf-jabba -profile singularity -c lsf.config --input samplesheet_jabba_nf.csv --outdir ${out_dir}  --tools svaba,hetpileups,fragcounter,dryclean,cbs,ascat,jabba --genome GATK.GRCh38 --step sv_calling -resume

Relevant files

samplesheet_jabba_nf.csv columns:
bam,bai,sample,patient,status

System information

Nextflow version: 23.10.0
OS: Rocky Linux 8.5
Hardware: HPC
Executor: LSF
Version mskilab-org/nf-jabba: v1.0dev-g90a4c70