define_cohort.task.yaml

name: Define Cohort
description: Create or update a cohort definition file specifying the name, series, included samples, filtering rules, and annotation track parameters.

agent_requirements:
  cpu_cores: 0
  memory_gb: 0

parameters:
  - name: cohort_name
    type: string
    label: Cohort Name
    help: The name of the cohort to create
    value: "Cohort"

  - name: series_name
    type: string
    label: Series Name
    help: The name of the series to create
    value: "cohort"

  - name: sample_name_threshold
    type: integer
    label: Sample Name Threshold
    help: The maximum number of sample names to list for rare variants
    value: 20

  - name: merge_step_file_count
    type: integer
    label: The number of files to merge at a time in each vcf merge step
    help: This can be adjusted to ensure that the performance stays within the bounds of the runner
    value: 128 

  - name: info_filter
    type: string
    label: Filter Expression (INFO fields)
    help: INFO field symbol names, comparisons (>, <, >=, <=, ==, !=), (and, or), operators (/ , +, - , * , ~) and values
    value: 'all( FILTER == "MLrejected" )'
    optional: true

  - name: format_filter
    type: string
    label: Filter Expression (FORMAT fields)
    help: FORMAT field symbol names, comparisons (>, <, >=, <=, ==, !=), (and, or), operators (/ , +, - , * , ~) and values
    value: "DP > 2"
    optional: true

steps:
  - name: create_cohort
    description: Create the initial cohort
    type: cmd
    command: bash
    args:
      - |- # shell
        #!/usr/bin/env bash
        set -e

        cohorts_folder="AppData/Common Data/UserAnnotations/cohorts"

        #
        # Parameters for track being created
        #
        sourceName="${cohort_name} Variant Frequencies"
        seriesName="${series_name}"

        #
        # Choose an output file base name and path. The base name will be extended with the current date and time.
        #
        out_file="${seriesName}.tsf"
        out_file="${cohorts_folder}/${out_file}"

        mkdir -p "${WORKSPACE_DIR}/${cohorts_folder}"
        out_parameter_file="${WORKSPACE_DIR}/${cohorts_folder}/${seriesName}-${cohort_name}.params.txt"

        echo "cohort_name=${cohort_name}" > "${out_parameter_file}"
        echo "series_name=${series_name}" >> "${out_parameter_file}"
        echo "out_file=${out_file}" >> "${out_parameter_file}"
        echo "sample_name_threshold=${sample_name_threshold}" >> "${out_parameter_file}"
        echo "info_filter=${info_filter}" >> "${out_parameter_file}"
        echo "format_filter=${format_filter}" >> "${out_parameter_file}"
        echo "merge_step_file_count=${merge_step_file_count}" >> "${out_parameter_file}"

        echo "Settings file created ${out_parameter_file}:"
        cat "${out_parameter_file}"