#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow inputs: # Intervals should come from capture kit (target intervals) bed format target_intervals: File[]? # Intervals should come from capture kit (bait intervals) bed format bait_intervals: File[]? reference_genome: type: File secondaryFiles: - .amb - .ann - .bwt - .pac - .sa - .fai - ^.dict outputs: target_interval_list: type: File outputSource: make_target_interval_list/output_interval_list_file bait_interval_list: type: File outputSource: make_bait_interval_list/output_interval_list_file steps: make_target_interval_list: run: ../tools/picard/picard-BedToIntervalList.cwl requirements: - class: ResourceRequirement coresMin: 1 ramMin: 4000 outdirMin: 12000 tmpdirMin: 12000 in: input_file: target_intervals reference_sequence: reference_genome out: - output_interval_list_file make_bait_interval_list: run: ../tools/picard/picard-BedToIntervalList.cwl requirements: - class: ResourceRequirement coresMin: 1 ramMin: 4000 outdirMin: 12000 tmpdirMin: 12000 in: input_file: bait_intervals reference_sequence: reference_genome out: - output_interval_list_file