3 label: RNAseq CWL practice workflow
12 run: bio-cwl-tools/fastqc/fastqc_2.cwl
21 run: bio-cwl-tools/STAR/STAR-Align.cwl
23 RunThreadN: {default: 4}
26 OutSAMtype: {default: BAM}
27 OutSAMunmapped: {default: Within}
31 run: bio-cwl-tools/samtools/samtools_index.cwl
33 bam_sorted: STAR/alignment
34 out: [bam_sorted_indexed]
36 ### 8. Adding it to the workflow
41 run: featureCounts.cwl
43 counts_input_bam: samtools/bam_sorted_indexed
50 outputSource: fastqc/html_file
53 outputSource: samtools/bam_sorted_indexed
55 # Adding it to the workflow
58 outputSource: featureCounts/featurecounts