+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+cwlVersion: v1.1
+class: Workflow
+label: Scatter to convert one chromosome of bam to fastqs
+requirements:
+ ScatterFeatureRequirement: {}
+
+inputs:
+ bams:
+ type:
+ type: array
+ items: File
+ format: edam:format_2572 # BAM
+ secondaryFiles: [.bai]
+ label: Alignments in BAM format
+ samples:
+ type:
+ type: array
+ items: string
+ label: Sample names
+ chrom:
+ type: string
+ label: Chromosome name
+
+outputs:
+ fastq1s:
+ type:
+ type: array
+ items: File
+ format: edam:format_1930 # FASTQ
+ label: One of set of pair-end FASTQs (R1)
+ outputSource: bam2singlechromfastq/fastq1
+ fastq2s:
+ type:
+ type: array
+ items: File
+ format: edam:format_1930 # FASTQ
+ label: One of set of pair-end FASTQs (R2)
+ outputSource: bam2singlechromfastq/fastq2
+
+steps:
+ bam2singlechromfastq:
+ run: bam2singlechromfastq.cwl
+ scatter: [bam, sample]
+ scatterMethod: dotproduct
+ in:
+ bam: bams
+ sample: samples
+ chrom: chrom
+ out: [fastq1, fastq2]