metrics.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0

class: Workflow

requirements:
  - class: InlineJavascriptRequirement

inputs:
  - id: bam
    type: File
  - id: known_snp
    type: File
  - id: fasta
    type: File
  - id: input_state
    type: string
  - id: parent_bam
    type: string
  - id: thread_count
    type: long
  - id: job_uuid
    type: string

outputs:
  - id: merge_sqlite_destination_sqlite
    type: File
    outputSource: merge_sqlite/destination_sqlite

steps:
  # - id: get_bam_readgroups
  #   run: ../../tools/get_bam_readgroups.cwl
  #   in:
  #     - id: bam
  #       source: bam
  #   out:
  #     - id: readgroups

  # - id: get_bam_library
  #   run: ../../tools/get_bam_library.cwl
  #   in:
  #     - id: readgroups
  #       source: get_bam_readgroups/readgroups
  #   out:
  #     - id: library

  # - id: get_bam_exome_kit
  #   run: ../../tools/get_bam_exome_kit.cwl
  #   in:
  #     - id: bam
  #       source: parent_bam
  #     - id: library
  #       source: get_bam_library/library
  #   out:
  #     - id: exome_kit

  # - id: get_bait_target
  #   run: ../../tools/get_bait_target.cwl
  #   in:
  #     - id: exome_kit
  #       source: get_bam_exome_kit/exome_kit
  #   out:
  #     - id: bait
  #     - id: target

  # - id: picard_collecthsmetrics
  #   run: ../../tools/picard_collecthsmetrics.cwl
  #   in:
  #     - id: BAIT_INTERVALS
  #       source: get_bait_target/bait
  #     - id: INPUT
  #       source: bam
  #     - id: OUTPUT
  #       source: bam
  #       valueFrom: $(self.basename + ".metrics")
  #     - id: REFERENCE_SEQUENCE
  #       source: fasta
  #     - id: TARGET_INTERVALS
  #       source: get_bait_target/target
  #   out:
  #     - id: METRIC_OUTPUT

  # - id: picard_collecthsmetrics_to_sqlite
  #   run: ../../tools/picard_collecthsmetrics_to_sqlite.cwl
  #   in:
  #     - id: bam
  #       source: bam
  #       valueFrom: $(self.basename)
  #     - id: bam_library
  #       source: get_bam_library/library
  #     - id: exome_kit
  #       source: get_bam_exome_kit/exome_kit
  #     - id: fasta
  #       source: fasta
  #       valueFrom: $(self.basename)
  #     - id: input_state
  #       source: input_state
  #     - id: metric_path
  #       source: picard_collecthsmetrics/METRIC_OUTPUT
  #     - id: job_uuid
  #       source: job_uuid
  #   out:
  #     - id: log
  #     - id: sqlite

  - id: picard_collectmultiplemetrics
    run: ../../tools/picard_collectmultiplemetrics.cwl
    in:
      - id: DB_SNP
        source: known_snp
      - id: INPUT
        source: bam
      - id: REFERENCE_SEQUENCE
        source: fasta
    out:
      - id: alignment_summary_metrics
      - id: bait_bias_detail_metrics
      - id: bait_bias_summary_metrics
      - id: base_distribution_by_cycle_metrics
      - id: gc_bias_detail_metrics
      - id: gc_bias_summary_metrics
      - id: insert_size_metrics
      - id: pre_adapter_detail_metrics
      - id: pre_adapter_summary_metrics
      - id: quality_by_cycle_metrics
      - id: quality_distribution_metrics
      - id: quality_yield_metrics

  - id: picard_collectmultiplemetrics_to_sqlite
    run: ../../tools/picard_collectmultiplemetrics_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: fasta
        source: fasta
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: job_uuid
        source: job_uuid
      - id: vcf
        source: known_snp
        valueFrom: $(self.basename)
      - id: alignment_summary_metrics
        source: picard_collectmultiplemetrics/alignment_summary_metrics
      - id: bait_bias_detail_metrics
        source: picard_collectmultiplemetrics/bait_bias_detail_metrics
      - id: bait_bias_summary_metrics
        source: picard_collectmultiplemetrics/bait_bias_summary_metrics
      - id: base_distribution_by_cycle_metrics
        source: picard_collectmultiplemetrics/base_distribution_by_cycle_metrics
      - id: gc_bias_detail_metrics
        source: picard_collectmultiplemetrics/gc_bias_detail_metrics
      - id: gc_bias_summary_metrics
        source: picard_collectmultiplemetrics/gc_bias_summary_metrics
      - id: insert_size_metrics
        source: picard_collectmultiplemetrics/insert_size_metrics
      - id: pre_adapter_detail_metrics
        source: picard_collectmultiplemetrics/pre_adapter_detail_metrics
      - id: pre_adapter_summary_metrics
        source: picard_collectmultiplemetrics/pre_adapter_summary_metrics
      - id: quality_by_cycle_metrics
        source: picard_collectmultiplemetrics/quality_by_cycle_metrics
      - id: quality_distribution_metrics
        source: picard_collectmultiplemetrics/quality_distribution_metrics
      - id: quality_yield_metrics
        source: picard_collectmultiplemetrics/quality_yield_metrics
    out:
      - id: log
      - id: sqlite

  - id: picard_collectoxogmetrics
    run: ../../tools/picard_collectoxogmetrics.cwl
    in:
      - id: DB_SNP
        source: known_snp
      - id: INPUT
        source: bam
      - id: REFERENCE_SEQUENCE
        source: fasta
    out:
      - id: OUTPUT

  - id: picard_collectoxogmetrics_to_sqlite
    run: ../../tools/picard_collectoxogmetrics_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: fasta
        source: fasta
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: metric_path
        source: picard_collectoxogmetrics/OUTPUT
      - id: job_uuid
        source: job_uuid
      - id: vcf
        source: known_snp
        valueFrom: $(self.basename)
    out:
      - id: log
      - id: sqlite

  - id: picard_collectwgsmetrics
    run: ../../tools/picard_collectwgsmetrics.cwl
    in:
      - id: INPUT
        source: bam
      - id: REFERENCE_SEQUENCE
        source: fasta
    out:
      - id: OUTPUT

  - id: picard_collectwgsmetrics_to_sqlite
    run: ../../tools/picard_collectwgsmetrics_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: fasta
        source: fasta
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: metric_path
        source: picard_collectwgsmetrics/OUTPUT
      - id: job_uuid
        source: job_uuid
    out:
      - id: log
      - id: sqlite

  - id: samtools_flagstat
    run: ../../tools/samtools_flagstat.cwl
    in:
      - id: INPUT
        source: bam
    out:
      - id: OUTPUT

  - id: samtools_flagstat_to_sqlite
    run: ../../tools/samtools_flagstat_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: metric_path
        source: samtools_flagstat/OUTPUT
      - id: job_uuid
        source: job_uuid
    out:
      - id: sqlite

  - id: samtools_idxstats
    run: ../../tools/samtools_idxstats.cwl
    in:
      - id: INPUT
        source: bam
    out:
      - id: OUTPUT

  - id: samtools_idxstats_to_sqlite
    run: ../../tools/samtools_idxstats_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: metric_path
        source: samtools_idxstats/OUTPUT
      - id: job_uuid
        source: job_uuid
    out:
      - id: sqlite

  - id: samtools_stats
    run: ../../tools/samtools_stats.cwl
    in:
      - id: INPUT
        source: bam
    out:
      - id: OUTPUT

  - id: samtools_stats_to_sqlite
    run: ../../tools/samtools_stats_to_sqlite.cwl
    in:
      - id: bam
        source: bam
        valueFrom: $(self.basename)
      - id: input_state
        source: input_state
      - id: metric_path
        source: samtools_stats/OUTPUT
      - id: job_uuid
        source: job_uuid
    out:
      - id: sqlite

  - id: merge_sqlite
    run: ../../tools/merge_sqlite.cwl
    in:
      - id: source_sqlite
        source: [
#          picard_collecthsmetrics_to_sqlite/sqlite,
          picard_collectmultiplemetrics_to_sqlite/sqlite,
          picard_collectoxogmetrics_to_sqlite/sqlite,
          picard_collectwgsmetrics_to_sqlite/sqlite,
          samtools_flagstat_to_sqlite/sqlite,
          samtools_idxstats_to_sqlite/sqlite,
          samtools_stats_to_sqlite/sqlite
        ]
      - id: job_uuid
        source: job_uuid
    out:
      - id: destination_sqlite
      - id: log