#!/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