chips_automator.config.yaml

###############################################################################
# Automator configuration file
###############################################################################

# Give the new instance a unique name, e.g. the chips run name
# NOTE: "chips-auto" will automatically be prepended to this string
instance_name: "test1"

# Define the number of cores for the chips instance
# Options- 32 (default), 64, 96 
cores: 32

# Define the disk size to use in GB, default 500
# the name of the persistent disk will be: "chips_auto_{instance_name}_disk"
disk_size: 500

#DEFINE the path to TRANSFER the files AFTER the chips run is complete
google_bucket_path: gs://mybucket/

# Uncomment the following and define the specific chips commit string to use
# chips_commit: 44b17ff
# chips_commit: develop

# DEFINE the samples- each sample should have a name, e.g. SAMPLE1
# and a Google bucket path to the input file, 
# e.g. gs://mybucket/data/sample1.fastq.gz
# VALID INPUTS: fastq, fastq.gz
# NOTE: for PAIRED-END fastq/fastq.gz, give both pairs to the sample:
# SAMPLE_1_PE:
#   - gs://mybucket/data/sample1_pair1.fastq
#   - gs://mybucket/data/sample1_pair2.fastq
samples:
  mocha2-Run1-pt1-Normal:
    - gs://mybucket/data/R1-1-N_HHTFLDSXX_R1.fastq.gz
    - gs://mybucket/data/R1-1-N_HHTFLDSXX_R2.fastq.gz
  mocha2-Run1-pt1-FF-Tumor:
    - gs://mybucket/data/R1-1-F_HHTFLDSXX_R1.fastq.gz
    - gs://mybucket/data/R1-1-F_HHTFLDSXX_R2.fastq.gz
  mocha2-Run1-pt1-FFPE-Tumor:
    - gs://mybucket/data/R1-1-FP_HHTFLDSXX_R1.fastq.gz
    - gs://mybucket/data/R1-1-FP_HHTFLDSXX_R2.fastq.gz

# metahseet- Group the samples into Treatment/Control "runs"
# each run should have a name, e.g. run_1:
# then under each run, define a Treatment and a Control sample
# EXAMPLE:
# metasheet:
#  run_1:
#    treat: SAMPLE_Tumor
#    cont: SAMPLE_normal
metasheet:
  mocha2-Run1-pt1-FF_run:
    treat: mocha2-Run1-pt1-Normal
    cont: mocha2-Run1-pt1-FF-Tumor
  mocha2-Run1-pt1-FFPE_run:
    treart: mocha2-Run1-pt1-Normal
    cont: mocha2-Run1-pt1-FFPE-Tumor