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bam_to_trimmed_fastq_and_biscuit_alignments.cwl
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bam_to_trimmed_fastq_and_biscuit_alignments.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "bam to trimmed fastqs and biscuit alignments"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
adapters:
type: File
adapter_trim_end:
type: string
adapter_min_overlap:
type: int
max_uncalled:
type: int
min_readlength:
type: int
read_group_id:
type: string
reference_index:
type: string
outputs:
aligned_bam:
type: File
outputSource: biscuit_markdup/markdup_bam
steps:
bam_to_fastq:
run: ../tools/bam_to_fastq.cwl
in:
bam: bam
out:
[fastq1, fastq2]
trim_fastq:
run: ../tools/trim_fastq.cwl
in:
reads1: bam_to_fastq/fastq1
reads2: bam_to_fastq/fastq2
adapters: adapters
adapter_trim_end: adapter_trim_end
adapter_min_overlap: adapter_min_overlap
max_uncalled: max_uncalled
min_readlength: min_readlength
out:
[fastq1, fastq2]
biscuit_align:
run: ../tools/biscuit_align.cwl
in:
reference_index: reference_index
fastq1: trim_fastq/fastq1
fastq2: trim_fastq/fastq2
read_group_id: read_group_id
out:
[aligned_bam]
index_bam:
run: ../tools/index_bam.cwl
in:
bam: biscuit_align/aligned_bam
out:
[indexed_bam]
biscuit_markdup:
run: ../tools/biscuit_markdup.cwl
in:
bam: index_bam/indexed_bam
out:
[markdup_bam]