4 label: RNAseq CWL practice workflow
15 run: bio-cwl-tools/fastqc/fastqc_2.cwl
20 # Running alignment with STAR
22 run: bio-cwl-tools/STAR/STAR-Align.cwl
24 RunThreadN: {default: 4}
27 OutSAMtype: {default: BAM}
28 SortedByCoordinate: {default: true}
29 OutSAMunmapped: {default: Within}
34 run: bio-cwl-tools/samtools/samtools_index.cwl
36 bam_sorted: STAR/alignment
37 out: [bam_sorted_indexed]
43 outputSource: fastqc/html_file
46 outputSource: samtools/bam_sorted_indexed