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alignment_umi_duplex.cwl
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alignment_umi_duplex.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "umi duplex alignment fastq workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "sequence: sequencing data and readgroup information"
doc: |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying
readgroup information. Note that in the @RG field ID and SM are required for FASTQs.
For BAMs, this pipeline assumes that the RG information is already in the header.
sample_name:
type: string
read_structure:
type: string[]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
target_intervals:
type: File?
outputs:
aligned_bam:
type: File
secondaryFiles: [^.bai]
outputSource: alignment_workflow/aligned_bam
adapter_histogram:
type: File[]
outputSource: alignment_workflow/adapter_histogram
duplex_seq_metrics:
type: File[]
outputSource: alignment_workflow/duplex_seq_metrics
steps:
sequence_to_bam:
scatter: [sequence]
scatterMethod: dotproduct
run: ../tools/sequence_to_bam.cwl
in:
sequence: sequence
out:
[bam]
alignment_workflow:
run: ../subworkflows/duplex_alignment.cwl
in:
bam: sequence_to_bam/bam
sample_name: sample_name
read_structure: read_structure
reference: reference
target_intervals: target_intervals
out:
[aligned_bam, adapter_histogram, duplex_seq_metrics]