tumor_only.yaml

# samples: a map of sample name to a list of Google bucket paths to input files,
# VALID INPUTS: fastq, fastq.gz, bam
# NOTE: for PAIRED-END fastq/fastq.gz, give both pairs to the sample
samples:
  C3RX3ZSEU.01:

    # r1
  - gs://repro_s1609_len/WES/fastq/concat_all/analysis/concat/C3RX3ZSEU.01_R1.fastq.gz



    # r2
  - gs://repro_s1609_len/WES/fastq/concat_all/analysis/concat/C3RX3ZSEU.01_R2.fastq.gz

  C3RX3ZS7Q.01:
  - gs://repro_s1609_len/WES/fastq/concat_all/analysis/concat/C3RX3ZS7Q.01_R1.fastq.gz
  - gs://repro_s1609_len/WES/fastq/concat_all/analysis/concat/C3RX3ZS7Q.01_R2.fastq.gz




# metasheet: Group the samples into Tumor-only "runs"
# each run should have a name, e.g. run_1 or tumor CIMAC ID:
# then under each run, define a tumor and a normal sample
metasheet:
  C3RX3ZSEU.01:
    tumor: C3RX3ZSEU.01

# unique instance name
instance_name: c3rx3zseu-01
# NOTE: "wes-auto" will automatically be prepended to this string

# Number of cores for the wes instance
# Options- 32 (default), 64, 96
cores: 64

# Disk size to use, in GB, default 750
disk_size: 500
# the name of the persistent disk will be: "wes_auto_{instance_name}_disk"

# CIMAC center the samples associate with
# Options- broad (.bam), mda (.fastq or fastq.gz)

cimac_center: 'mda'


# Trim soft clip reads when calling somatic variants?
# Not available for tnsnv
# Default: trim_soft_clip: False
trim_soft_clip: false

# tumor_only - IF the normal sample is NOT available
# The normal samples are empty in the metasheet above.
tumor_only: true

# Somatic variant caller preference
# Options- tnscope (default), tnsnv, tnhaplotyper2
somatic_caller: 'tnscope'

# IGNORED Path to the google bucket path for the run
# google_bucket_path: gs://...

# Specific wes commit string to use (filled by pipeline team)
# wes_commit:

# Specific wes google image to use (filled by pipeline team)
# image:

# Specific wes reference snapshot to use (filled by pipeline team)
# wes_ref_snapshot:
sentieon_path: '/home/taing/sentieon/sentieon-genomics-202010.01/bin/'
wes_ref_snapshot: 'wes-human-ref-ver1-5a'
image: 'wes-ver2-24a'
wes_commit: '4679213'
google_bucket_path: 'gs://repro_s1609_len/WES/C3RX3ZSEU.01/'