config.json

{
    "NGS_workspace": "/Volumes/Samsung_T5/ngs/",

    "bio_pipe_alignment_spark_num_executors": 5,
    "bio_pipe_alignment_spark_executor_memory": "12g",
    "bio_pipe_alignment_spark_executor_memory": "12g",
    "bio_pipe_alignment_spark_driver_memory": "12g",

    "bio_pipe_variantcalling_spark_num_executors": 5,
    "bio_pipe_variantcalling_spark_executor_memory": "12g",
    "bio_pipe_variantcalling_spark_executor_memory": "12g",
    "bio_pipe_variantcalling_spark_driver_memory": "12g",
    "freebayes_docker_image": null,

    "bio_pipe_annotation_spark_num_executors": 5,
    "bio_pipe_annotation_spark_executor_memory": "12g",
    "bio_pipe_annotation_spark_executor_memory": "12g",
    "bio_pipe_annotation_spark_driver_memory": "12g",
    "bio_pipe_vep_cache": "/Volumes/Samsung_T5/ngs/vep/98/",
    "vep_docker_image": "quay.io/biocontainers/ensembl-vep:98.2--pl526hecc5488_0",


    "bio_pipe_cannoli": "/Users/dominika/projects/cannoli/assembly/target/cannoli-assembly-spark3_2.12-0.11.0-SNAPSHOT.jar",
    "bio_pipe_reference": "/Volumes/Samsung_T5/ngs/reference/genome.fa",
    "bio_pipe_jar": "/Users/dominika/assembly_with_bqsr.jar",
    "bio_pipe_adam_jar": "/data/work/home/dmaziec/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar",
    "bio_pipe_spark_connection": "cdh00",
    "bio_pipe_aligner": "bwa",
    "bio_pipe_snps_file": "/Volumes/Samsung_T5/ngs/bqsr1.vcf"
}