Pipeline YAML

You may configure the pipeline parameters in a YAML file.

• validation Validations to be performed before even creating an analysis
  • optional Optional validation, user will get an option to ignore warnings
  • required Required validation, user will not be able to start analysis

Here are a list of possible validations and accepted values. These validations maybe added to either the optional or required sections.

• datatype accepts multiple values as list, e.g, rna-seq, chip-seq, etc
• filetypes accepts multiple values as list, e.g, bam, fastq, etc
• genome if true, all samples must have a genome set
• num_samples number of samples accepted by the pipeline, possible values are 0, 1 (exactly 1) and 1+ (one or more).
• num_controls number of controls accepted by the pipeline, possible values are same as num_samples.

Example configuration

In this example, if the data type is other than rna-seq, users gets a warning. The only accepted file types in the sample are fastq and bam. Each sample must have a genome assigned and the pipeline will run on a single sample.

validation:
  optional:
    datatype:
      - rna-seq
  required:
    filetypes:
      - fastq
      - bam
    genome: true
    num_samples: '1'
    num_controls: '0'