3 label: RNAseq Alignment workflow
11 StepInputExpressionRequirement: {}
26 RunThreadN: {default: 4}
29 OutSAMtype: {default: BAM}
30 SortedByCoordinate: {default: true}
31 OutSAMunmapped: {default: Within}
32 OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
36 run: samtools_index.cwl
38 bam_sorted: STAR/alignment
39 out: [bam_sorted_indexed]
44 outputSource: fastqc/html_file
47 outputSource: samtools/bam_sorted_indexed