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class: Workflow
id: "bwa-mem-0.15 to samtools view"
label: "WorkFlowTest v1.0"
cwlVersion: v1.0
#dct:creator:{'@id': 'http://orcid.org/0000-0003-0342-8531', 'foaf:name': Adelaide Rhodes,
#'foaf:mbox': mailto:adelaide.rhodes@gmail.com}
inputs:
- id : M_flag
type: boolean
default: true
- id: fastq1
type: File
doc: "Required first fastq file"
- id: fastq2
type: File?
doc: "Optional second fastq file"
- id: fasta
type: File
doc: "BWA Indexed reference fasta file with secondary files in same directory"
secondaryFiles:
- ".amb"
- ".ann"
- ".pac"
- ".bwt"
- ".sa"
- id: output_filename
type: string
- id: threads
type: int
outputs:
- id: output
type: File
doc: "Alignments in BAM format"
outputSource: samtoolsview/output
steps:
- id: bwamem
in:
- { id: M_flag, source: "M_flag" }
- { id: fastq1, source: "#fastq1" }
- { id: fastq2, source: "#fastq2"}
- { id: fasta, source: "#fasta" }
- { id: threads, source: "#threads" }
out:
- { id: output.sam }
run: BWAMEM.cwl
- id: samtoolsview
in:
- { id: input, source: "#bwamem/output.sam" }
- { id: output_name, source: "#output_filename" }
out:
- { id: output }
run: SAMTOOLS-VIEW.cwl
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