rnaseq.yaml

# The following section contains static files required by the pipeline
resources:
  adapters: /data/groups/lab_bock/shared/resources/adapters/nextera_adapters.fa
  kallisto_index:
    hg38: /data/groups/lab_bock/shared/resources/genomes/hg38_cdna/indexed_kallisto/hg38_cdna.idx
    hg38_cdna: /data/groups/lab_bock/shared/resources/genomes/hg38_cdna/indexed_kallisto/hg38_cdna.idx
    hg19: /data/groups/lab_bock/shared/resources/genomes/hg19_cdna/indexed_kallisto/hg19_cdna.idx
    hg19_cdna: /data/groups/lab_bock/shared/resources/genomes/hg19_cdna/indexed_kallisto/hg19_cdna.idx
    mm10: /data/groups/lab_bock/shared/resources/genomes/mm10_cdna/indexed_kallisto/mm10_cdna.idx
    mm10_cdna: /data/groups/lab_bock/shared/resources/genomes/mm10_cdna/indexed_kallisto/mm10_cdna.idx
    mm9: /data/prod/ngs_resources/genomes/mm9_cdna/indexed_kallisto/mm9_cdna.idx
    mm9_cdna: /data/prod/ngs_resources/genomes/mm9_cdna/indexed_kallisto/mm9_cdna.idx
    ercc: /data/groups/lab_bock/shared/resources/genomes/ERCC92_cdna/indexed_kallisto/ERCC92_cdna.idx
    ercc_cdna: /data/groups/lab_bock/shared/resources/genomes/ERCC92_cdna/indexed_kallisto/ERCC92_cdna.idx


# The following section contains command-line tools used by the pipeline
tools:
  fastqc: fastqc
  java: java
  picard: /cm/shared/apps/picard-tools/1.140/picard.jar
  samtools: samtools
  sambamba: sambamba
  trimmomatic: trimmomatic
  skewer: skewer
  kallisto: kallisto


# The following section parameters used to control pipeline behaviour
parameters:
  # which trimmer to use:
  # choose between ["trimmomatic", "skewer"]
  trimmer: "skewer"
  # Number of sampling bootstraps to perform.
  bootstrap_number: 100
  # Mean fragment size of library. Only required if `read_type` is 'single'.
  fragment_size: 300
  # Standard deviation of libray fragment size. Only required if `read_type` is 'single'.
  fragment_std: 200