Notice: all the docker tages are temporarily removed due to the log4j vulnerability. The workflow can not be run as is until the log4j issue is resolved.

GenoMEL-Bionimbus Protected Data Cloud (PDC) production pipeline

General workflow:

GenoMEL individual aliquot workflow:

• Individual CWL workflow runner

• Individual CWL runner input json template

• Individual workflow SLURM python runner

• individual workflow SLURM SBATCH job template

GenoMEL cohort genotyping workflow

• Cohort level CWL workflow runner

• Cohort level CWL runner input json template

• Cohort level SLURM python runner

• Cohort level SLURM SBATCH job template