5 ### 2. Command line tool inputs
10 ### 3. Specifying the program to run
11 baseCommand: featureCounts
13 ### 4. Command arguments
14 arguments: [-T, $(runtime.cores),
16 -o, featurecounts.tsv,
17 $(inputs.counts_input_bam)]
19 ### 5. Outputs section
24 glob: featurecounts.tsv
26 ### 6. Running in a container
29 dockerPull: quay.io/biocontainers/subread:1.5.0p3--0