workdir: workspace
# can be "ECLIP10", "ECLIP6", "TAKARAV3", "SACSEQV3", "STRANDED"
libtype: ECLIP10
# TODO: if the genome index is not available, the pipeline will build it automatically
genome_index: /data/reference/genome/Arabidopsis_thaliana/hisat2_tx_3n/TAIR10.release57
reference:
  contamination:
    # Multiple contaminant reference files are allowed
    - ref/Agrobacterium.fa.gz
  genes:
    # Multiple gene reference files are allowed
    - ref/spikein.fa
    - ref/ERCC92.fa
    - ref/cress_rRNA.fa
  genome:
    # Only one genome is allowed
    - /data/reference/genome/Arabidopsis_thaliana/TAIR10.fa
samples:
  cress1:
    data:
      - R1: data/cress1_R1.fq.gz
        R2: data/cress1_R2.fq.gz
  cress2:
    data:
      - R1: data/cress2_R1.fq.gz
        R2: data/cress2_R2.fq.gz