I’m fairly new to CWL. I’ve been able to get my head around some of the ways that CWL works and have read the examples, etc. I’m trying to build a pipeline in which all steps are executed within Docker containers. I have several steps working. However, I am stumped on something super simple. Maybe this seems silly, but I’m trying to remove a file. Below is my workflow file.
#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool baseCommand: rm requirements: - class: DockerRequirement dockerPull: phusion/baseimage:master-amd64 - class: InitialWorkDirRequirement listing: - entry: $(inputs.the_file) writable: true inputs: the_file: type: File inputBinding: prefix: -f position: 1 outputs: output: stdout stdout: output.txt
Below is my job file:
the_file: class: File path: Genome/Zea_mays.B73_RefGen_v4.dna.toplevel.fa
It says it was successful, but the file is still there. What am I missing? Is there a simpler/better way?