--- /dev/null
+cwlVersion: v1.2
+class: Workflow
+label: RNAseq CWL practice workflow
+
+inputs:
+ fq: File
+ genome: Directory
+ gtf: File
+
+requirements:
+ StepInputExpressionRequirement: {}
+
+steps:
+ fastqc:
+ run: bio-cwl-tools/fastqc/fastqc_2.cwl
+ in:
+ reads_file: fq
+ out: [html_file]
+
+ STAR:
+ requirements:
+ ResourceRequirement:
+ ramMin: 9000
+ run: bio-cwl-tools/STAR/STAR-Align.cwl
+ in:
+ RunThreadN: {default: 4}
+ GenomeDir: genome
+ ForwardReads: fq
+ OutSAMtype: {default: BAM}
+ SortedByCoordinate: {default: true}
+ OutSAMunmapped: {default: Within}
+ ### 1. Expressions on step inputs
+ OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
+ out: [alignment]
+
+ samtools:
+ run: bio-cwl-tools/samtools/samtools_index.cwl
+ in:
+ bam_sorted: STAR/alignment
+ out: [bam_sorted_indexed]
+
+outputs:
+ qc_html:
+ type: File
+ outputSource: fastqc/html_file
+ bam_sorted_indexed:
+ type: File
+ outputSource: samtools/bam_sorted_indexed