# Cancer tumor/normal calling evaluation using synthetic dataset 3
# from the ICGC-TCGA DREAM challenge:
# https://www.synapse.org/#!Synapse:syn312572/wiki/62018
---
details:
- algorithm:
    aligner: bwa
    exclude_regions: [lcr]
    mark_duplicates: true
    variantcaller: [mutect2, vardict]
    variant_regions: /path/to/bcbio/genomes/Hsapiens/hg38/coverage/capture_regions/NGv3.bed
    # svcaller: [cnvkit, lumpy, delly]
    # coverage_interval: amplicon
  analysis: variant2
  description: syn3-normal
  #files: ../input/synthetic.challenge.set3.normal.bam
  files:
    - ../input/synthetic_challenge_set3_normal_NGv3_1.fq.gz
    - ../input/synthetic_challenge_set3_normal_NGv3_2.fq.gz
  genome_build: hg38
  metadata:
    batch: syn3
    phenotype: normal
- algorithm:
    aligner: bwa
    exclude_regions: [lcr]
    mark_duplicates: true
    variantcaller: [mutect2, vardict]
    variant_regions: /path/to/bcbio/genomes/Hsapiens/hg38/coverage/capture_regions/NGv3.bed
  analysis: variant2
  description: syn3-tumor
  #files: ../input/synthetic.challenge.set3.tumor.bam
  files:
    - ../input/synthetic_challenge_set3_tumor_NGv3_1.fq.gz
    - ../input/synthetic_challenge_set3_tumor_NGv3_2.fq.gz
  genome_build: hg38
  metadata:
    batch: syn3
    phenotype: tumor
upload:
  dir: ../final