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Pipeline configuration files

If you write a pipeline config file in yaml format and name it the same thing as the pipeline (but replacing .py with .yaml), pypiper will automatically load and provide access to these configuration options, and make it possible to pass customized config files on the command line. This is very useful for tweaking a pipeline for a similar project with slightly different parameters, without having to re-write the pipeline.

It's easy: just load the PipelineManager with args (as described in command-line arguments), and you have access to the config file automatically in in pipeline.config.

For example, in you write:

parser = pypiper.add_pipeline_args(parser, args=["config"])
pipeline = pypiper.PipelineManager(name="my_pipeline", outfolder=outfolder, \
                    args = parser)

And in the same folder, you include myscript.yaml:

  setting1: True
  setting2: 15

Then you can access these settings automatically in your script using:


This yaml file is useful for any parameters not related to the input Sample (which should be passed on the command-line). By convention, for consistency across pipelines, we use sections called tools, resources, and parameters, but the developer has the freedom to add other sections/variables as needed.

Here's a more realist example pipeline configuration file:

# paths to required tools
  java:  "/home/user/.local/tools/java"
  trimmomatic:  "/home/user/.local/tools/trimmomatic.jar"
  fastqc:  "fastqc"
  samtools:  "samtools"
  bsmap:  "/home/user/.local/tools/bsmap"
  split_reads:  "/home/user/.local/tools/"

# paths to reference genomes, adapter files, and other required shared data
  resources: "/data/groups/lab_bock/shared/resources"
  genomes: "/data/groups/lab_bock/shared/resources/genomes/"
  adapters: "/data/groups/lab_bock/shared/resources/adapters/"

# parameters passed to bioinformatic tools, subclassed by tool
    quality_encoding: "phred33"
    threads: 30
      adapter_fasta: "/home/user/.local/tools/resources/cpgseq_adapter.fa"
      seed_mismatches: 2
      palindrome_clip_threshold: 40
      simple_clip_threshold: 7
      window_size: 4
      required_quality: 15
      target_length: 17
      strictness: 0.5
      min_length: 17
    seed_size: 12
    mismatches_allowed_for_background: 0.10
    mismatches_allowed_for_left_splitreads: 0.06
    mismatches_allowed_for_right_splitreads: 0.00
    equal_best_hits: 100
    quality_threshold: 15
    quality_encoding: 33
    max_number_of_Ns: 3
    processors: 8
    random_number_seed: 0
    map_to_strands: 0