4 label: RNAseq CWL practice workflow
15 run: bio-cwl-tools/fastqc/fastqc_2.cwl
20 ### 4. Running alignment with STAR
25 run: bio-cwl-tools/STAR/STAR-Align.cwl
27 RunThreadN: {default: 4}
30 OutSAMtype: {default: BAM}
31 OutSAMunmapped: {default: Within}
34 ### 5. Running samtools
36 run: bio-cwl-tools/samtools/samtools_index.cwl
38 bam_sorted: STAR/alignment
39 out: [bam_sorted_indexed]
41 ### 7. Workflow Outputs
45 outputSource: fastqc/html_file
48 outputSource: samtools/bam_sorted_indexed