test.config

params {
  outdir = "result_test"
  // input for hashing-based deconvolution
  hto_matrix_raw = "$projectDir/test_data/hto_gz"
  hto_matrix_filtered = "$projectDir/test_data/hto_gz"
  rna_matrix_raw = "$projectDir/test_data/rna"
  rna_matrix_filtered = "$projectDir/test_data/rna"

  // input for genotype-based deconvolution
  bam = "$projectDir/test_data/jurkat_293t_downsampled_n500_full_bam.bam"
  bai = "$projectDir/test_data/jurkat_293t_downsampled_n500_full_bam.bam.bai"
  barcodes = "$projectDir/test_data/barcodes.tsv"
  fasta = "$projectDir/test_data/genome_chr1.fa"
  fasta_index = "$projectDir/test_data/genome_chr1.fa.fai"
  nsamples_genetic = 2
  common_variants_scSplit = "$projectDir/test_data/common_variants_hg19_list.vcf"
  common_variants_souporcell =  "$projectDir/test_data/common_variants_hg19.vcf"
  common_variants_freemuxlet = "$projectDir/test_data/jurkat_293t_exons_only.vcf.withAF.vcf.gz"
  common_variants_cellsnp  = "$projectDir/test_data/genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz"
  vcf_donor = "$projectDir/test_data/jurkat_293t_exons_only.vcf.withAF.vcf"
  // Call freebayes on chr 1 and chr 2 only to speed up run time
  region = "1"
  // donor genotype file provided by popscle doesnt work on souporcell
  use_known_genotype = "False"
  ignore = "True"
  //gmm_demux input
  hto_name_gmm = "hto_1,hto_2"

}