#!/usr/bin/env eCLIP_pairedend_singlenode

dataset: "204_01"

speciesGenomeDir:
  class: Directory
  path: /home/centos/refs/STAR

repeatElementGenomeDir:
  class: Directory
  path: /home/centos/refs/STAR_repeat/

species: hg19

chrom_sizes:
  class: File
  path: /home/centos/refs/STAR/chrNameLength.txt

barcodesfasta:
  class: File
  path: /home/centos/eclip/example/inputs/yeolabbarcodes_20170101.fasta

randomer_length: "5"

samples:
  -
    - ip_read:
      name: rep1_clip
      barcodeids: [A01, B06]
      read1:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-CLIP_S1_R1.fastq.gz
      read2:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-CLIP_S1_R2.fastq.gz

    - input_read:
      name: rep1_input
      barcodeids: [NIL, NIL]
      read1:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-INPUT_S2_R1.fastq.gz
      read2:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-INPUT_S2_R2.fastq.gz
  -
    - ip_read:
      name: rep2_clip
      barcodeids: [C01, D8f]
      read1:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-CLIP_S1_R1.fastq.gz
      read2:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-CLIP_S1_R2.fastq.gz

    - input_read:
      name: rep2_input
      barcodeids: [NIL, NIL]
      read1:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-INPUT_S2_R1.fastq.gz
      read2:
        class: File
        path: /home/centos/fastqs/RBFOX2-204-INPUT_S2_R2.fastq.gz