SV_Pipeline_Full.inputs.json

{
  "##_COMMENT1": "DATA INPUTS",
  "SV_Pipeline.aligned_crams": [
    "gs://mgi-wdl-test/data/call-Extract_Reads/shard-0/attempt-2/H_IJ-NA12878-NA12878_K10.cram",
    "gs://mgi-wdl-test/data/call-Extract_Reads/shard-1/attempt-4/H_IJ-NA12891-NA12891_D2.cram"
  ],
  "SV_Pipeline.cohort_name": "pilot-01",
  "SV_Pipeline.final_vcf_name": "pilot-01.vcf.gz",
  "SV_Pipeline.aligned_cram_suffix": ".cram",

  "##_COMMENT2": "REFERENCE FILES",
  "SV_Pipeline.ref_fasta": "gs://human-b38/GRCh38DH/all_sequences.fa",
  "SV_Pipeline.ref_fasta_index": "gs://human-b38/GRCh38DH/all_sequences.fa.fai",
  "SV_Pipeline.ref_cache": "gs://human-b38/cache.tar.gz",
  "SV_Pipeline.ref_dict": "gs://human-b38/GRCh38DH/all_sequences.dict",
  "SV_Pipeline.ref_alt": "gs://human-b38/GRCh38DH/all_sequences.fa.alt",
  "SV_Pipeline.exclude_regions": "gs://human-b38/GRCh38DH/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed",
  "SV_Pipeline.mei_annotation_bed": "gs://human-b38/GRCh38DH/annotations/repeatMasker.recent.lt200millidiv.LINE_SINE_SVA.GRCh38.sorted.bed.gz",

  "##_COMMENT3": "SYSTEM PARAMETERS",
  "SV_Pipeline.disk_size": 50,
  "SV_Pipeline.preemptible_tries": 3
}