Input files

Configuration

The pipeline-suite runs using parameters provided in YAML format. There are two types of required configuration files:

• data configs:

  • dna_fastq_config.yaml and rna_fastq_config.yaml
  • bam_config.yaml, generated by any tool which outputs BAMs that are required for downstream steps

• pipeline configs (dna_pipeline_config.yaml and rna_pipeline_config.yaml):

  • these specify common parameters, including:
    • project name
    • sequencing type (wgs, exome, rna or targeted), sequencing centre and platform
    • is_ctdna (true or false)
    • hpc_group to indicate group to use for job submission (ie, slurm -A group argument)
    • ref_type (ie, hg19 or hg38)
    • path to desired output directory (will be created if this is the initial run)
    • paths to tool-specific reference files/directories
    • desired versions of tools
  • and, for each tool, memory and run time parameters for each step

For tool-specific details for RNA-Seq configuration, click here: RNA-Seq.

For tool-specific details for DNA-Seq configuration, click here: DNA-Seq.