Hi everybody,

I have a problem with hard-coded paths in scripts that would require changing the directory before executing a command line tool.

Let's consider the following minimal example:

○ → tree
.
├── code
│   └── script.py
├── data
│   └── hi.txt
└── tool.cwl

with script.py:

#! /usr/bin/env python3

with open('../data/hi.txt', 'r') as f:
    for line in f:
        print(line)

When I run script.py from the /code diretory, it prints the content of hi.txt. I then try to wrap this into a CWL tool:

cwlVersion: v1.0
class: CommandLineTool

inputs:

  script:
    type: File
    inputBinding:
      position: 1
    default:
      class: File
      path: code/script.py

  data:
    type: File
    default:
      class: File
      path: data/hi.txt

outputs: []

requirements:
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.script)
        entryname: code/script.py
      - entry: $(inputs.data)
        entryname: data/hi.txt

Running this tool fails when the script tries to open hi.txt. I can fix this by changing into the right directory at the beginning of the script:

import os
os.chdir(os.path.dirname(os.path.abspath(__file__)))

Now I'm wondering if CWL offers a way to change the directory before executing a tool instead. I am aware that using arguments instead of hard-coded paths or at least making the paths relative to the root of my dummy project would help here. But let's just assume that I can not modify the script at all.

Thanks!