Pipeline configuration (config.yaml, resources.yaml)

Configuration of the pipeline is set up in the config.yaml file. Both general settings and rule specific settings are set here. The config.yaml can also point to other config-files, such as a config for reasources resources.yaml.

Basic setup

Basic setup for config.yaml:

resources: "config/resources.yaml"                          # resources parameters
samples: "samples.tsv"                                      # sample names
units: "units.tsv"                                          # sample file and meta info
output: "config/output_list.json"                           # rule all files (optional)
default_container: "docker://hydragenetics/common:0.1.9"    # default container
reference:                                                  # list of general references
  fasta: “reference_genome.fasta”

Basic setup for the resources.yaml for default resource usage:

default_resources:
  mem_mb: 6144        # total max memory
  mem_per_cpu: 6144   # memory per thread
  partition: "core"   # partition to us on the cluster (optional)
  threads: 1          # threads
  time: "4:00:00"     # wall time

Rule parameters

Rules with configurable parameters can be set in config.yaml in the following way:

cnvkit_batch:
  container: "docker://hydragenetics/cnvkit:0.9.9"  # container
  normal_reference: "cnvkit_panel_of_normal.cnn"    # reference file
  method: "hybrid"                                  # program parameter

Rules with extra resource demands can be set in resources.yaml in the following way:

arriba:
  mem_mb: 30720
  mem_per_cpu: 6144
  threads: 5
  time: "8:00:00"