Hi Michael! I have an R script that takes as input 3 files namely an OTU file, a map and a tree and generates a set of reports in the folder output and test.Rdata in current folder. At command line I call it as follows:
Rscript PhyloseqReport.R otus.tax.biom dog_stool_samples_metadata.tsv otus.tre output test.Rdata
I have started the following cwl script:
#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool inputs: otuFile: type: File inputBinding: position: 1 mapFile: type: File inputBinding: position: 2 tre: type: File inputBinding: position: 3 baseCommand: [ Rscript, PhyloSeqReport.R, "results.Rdata" ] outputs: results: type: File outputBinding: glob: results.Rdata
How do I capture the fact that the set of reports generated should go in folder output?