example_config.yml

workdir: "/exports/sasc/dcats/snakemake/testOut"
sampleSheet: "/exports/sasc/dcats/snakemake/testOut/sample.tsv"
reference:
  fasta: "/usr/local/Genomes/H.Sapiens/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa"
  gff: "/exports/genomes/species/H.sapiens/GRCh38_no_alt_analysis_set/annotation/features/ensembl_87/ensembl.87.gtf"
  refflat: "/exports/genomes/species/H.sapiens/GRCh38_no_alt_analysis_set/annotation/features/ensembl_87/ensembl.87.refflat"
  dbsnp: "/exports/genomes/species/H.sapiens/GRCh38_no_alt_analysis_set/annotation/dbsnp/dbsnp-149.vcf.gz"
mappers:
  star:
    index: "/exports/sasc/dcats/GRCh38_no_alt_anaylsis_set_ensembl_87_STAR_indexes"
  star2pass:
    index: "/exports/sasc/dcats/GRCh38_no_alt_anaylsis_set_ensembl_87_STAR_indexes"
  hisat2:
    index: "/exports/sasc/dcats/GRCh38_no_alt_analysis_set_HISAR2_indexes/ref"
counting:
  htseq-count: {}
  featurecounts: {}
  star_quantmode: {}
  basecounter_exon: {}
  basecounter_intron: {}
  basecounter_gene: {}
  basecounter_transcript: {}
  salmon:
    index: "/exports/sasc/dcats/GRCh38_ensemble_91_SALMON_indexes"
variantcalling:
  varscan: {}
  haplotypecaller: {}
centrifuge:
  index: "/exports/sasc/project-187-virobiom/refseq/index/refseq"