test.config.yaml

###############################################################################
# Automator configuration file
###############################################################################
#trim_soft_clip: False
#genes_to_plot: GAPDH ACTB TP53
#upstream: 50000
#downstream: 50000

#trim_adapter: true

# 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: 'chips-auto-fast-test'

# 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: 200

#DEFINE the path to TRANSFER the files AFTER the chips run is complete
google_bucket_path: gs://lens_bucket2/chips_automator/raw_data/test_set1/Results/

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

#Define the chips reference snapshot to use, default chips-ref-ver1-0
chips_ref_snapshot: 'chips-ref-ver1-1'

#Uncomment the following and define the specific chips GCP image to use
#NOTE: IF a specific GCP image is not set via config['image'], then
#the default behavior is to get the latest chips image
image: 'chips-ver1-10'

#ALIGNER: if you have sentieon license and got sentieon installed on your machine
#Uncomment the following line and set absolute path of sentieon
#This software could speed up your alignment
sentieon: "/home/taing/sentieon/sentieon-genomics-201808.05/bin/sentieon"

#genome trackview parameters
genes_to_plot: 'GAPDH ACTB TP53 IL7R CCR7 S100A4 CD8A CD14 MS4A1 GNLY'
upstream: 50000
downstream: 50000

# 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:
  wz2116:
    - gs://lens_bucket2/chips_automator/raw_data/test_set1/4433_2_wz2116_TGAAGAGA_S63_L007_R1_001.1mil.fastq.gz
  wz2130:
    - gs://lens_bucket2/chips_automator/raw_data/test_set1/4455_6_wz2130_ACAGCAGA_S35_L002_R1_001.1mil.fastq.gz
  wz2163:
    - gs://lens_bucket2/chips_automator/raw_data/test_set1/4455_39_wz2163_GGAGAACA_S68_L005_R1_001.1mil.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:
  wz2116:
    treat1: 'wz2116'
    cont1:
    treat2:
    cont2:
  wz2130:
    treat1: 'wz2130'
    cont1:
    treat2:
    cont2:
  wz2163:
    treat1: 'wz2163'
    cont1:
    treat2:
    cont2: