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#!/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
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