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amplicon_metrics.cwl
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amplicon_metrics.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/amplicon_kit.yml
inputs:
- id: bam
type: File
- id: amplicon_kit_set_file
type: ../../tools/amplicon_kit.yml#amplicon_kit_set_file
- id: fasta
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .fai
- .pac
- .sa
- ^.dict
- id: input_state
type: string
- id: job_uuid
type: string
outputs:
- id: sqlite
type: File
outputSource: picard_collecttargetedpcrmetrics_to_sqlite/sqlite
steps:
- id: picard_collecttargetedpcrmetrics
run: ../../tools/picard_collecttargetedpcrmetrics.cwl
in:
- id: AMPLICON_INTERVALS
source: amplicon_kit_set_file
valueFrom: $(self.amplicon_kit_amplicon_file)
- id: INPUT
source: bam
- id: OUTPUT
source: bam
valueFrom: $(self.basename).pcrmetrics
- id: REFERENCE_SEQUENCE
source: fasta
- id: TARGET_INTERVALS
source: amplicon_kit_set_file
valueFrom: $(self.amplicon_kit_target_file)
out:
- id: METRIC_OUTPUT
- id: picard_collecttargetedpcrmetrics_to_sqlite
run: ../../tools/picard_collecttargetedpcrmetrics_to_sqlite.cwl
in:
- id: bam
source: bam
valueFrom: $(self.basename)
- id: input_state
source: input_state
- id: metric_path
source: picard_collecttargetedpcrmetrics/METRIC_OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: log
- id: sqlite