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umi_molecular_alignment.cwl
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umi_molecular_alignment.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "umi molecular alignment fastq workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
read1_fastq:
type: File[]
read2_fastq:
type: File[]
sample_name:
type: string
library_name:
type: string[]
platform_unit:
type: string[]
platform:
type: string[]
read_structure:
type: string[]
reference:
type: string
target_intervals:
type: File?
outputs:
aligned_cram:
type: File
secondaryFiles: [.crai, ^.crai]
outputSource: alignment_workflow/aligned_cram
adapter_histogram:
type: File[]
outputSource: alignment_workflow/adapter_histogram
duplex_seq_metrics:
type: File[]
outputSource: alignment_workflow/duplex_seq_metrics
steps:
fastq_to_bam:
scatter: [read1_fastq, read2_fastq, library_name, platform_unit, platform]
scatterMethod: dotproduct
run: ../tools/fastq_to_bam.cwl
in:
read1_fastq: read1_fastq
read2_fastq: read2_fastq
sample_name: sample_name
library_name: library_name
platform_unit: platform_unit
platform: platform
out:
[bam]
alignment_workflow:
run: ../subworkflows/molecular_alignment.cwl
in:
bam: fastq_to_bam/bam
sample_name: sample_name
read_structure: read_structure
reference: reference
target_intervals: target_intervals
out:
[aligned_cram, adapter_histogram, duplex_seq_metrics]