How to specify a list of directory in InputWorkDirRequirement

[matmanc]

Hi, I am running in the following issue. I have a list of directory that I would like to modify as input.
To do so I add them in the InputWorkDirRequirement but for some reason it only works for a single directory.

This is my cwl workflow

    class: CommandLineTool
    cwlVersion: v1.1
    id: test_multiple_dir_input
    baseCommand:
      - /bin/bash
      - script.sh
    inputs:
      - id: msin
        type: 'Directory[]'
    outputs: 
      - id: std_out
        type: File
        outputBinding:
          glob: test_multiple_dir_input.log
    label: test_multiple_dir_input
    requirements:
      - class: DockerRequirement
        dockerPull: 'lofareosc/prefactor:HBAcalibrator'
      - class: InitialWorkDirRequirement
        listing:
          - entry: $(inputs.msin)
            writable: true
          - entryname: script.sh
            entry: | 
              #!/bin/bash
              ls -lR
              rm test1/dude.txt
      - class: InlineJavascriptRequirement
    stdout: test_multiple_dir_input.log

and this is my input file

{
    "msin": [{"class": "Directory", "path":"test1"}, {"class": "Directory", "path":"test2"}]
}

the directory listing is the following:

[15:10:07] mmancini:multiple_folders $ ls -lR test1 test2  
test1:
total 0
-rw-rw-r-- 1 mmancini mmancini 0 Feb 22 15:10 dude.txt

test2:
total 0

This is obviously a minimum snippet to recreate the problem.

To execute the workflow I am using cwltool with version 3.0.20210124104916

[steve]

Not sure if its exactly the same problem but this sounds kinda similar to the issue I was having here;

How to create a UUID inside CWL?

Due to the issue described here where input files with the same basename cause errors with a directory InitialWorkDirRequirement, I need to find a way to generate unique filenames that will not conflict with each other. Ideally, I would just use a Javascript expression inside my CWL to accomplish this, but I could not get any of these suggested methods to generate random strings to work (or they required huge amounts of custom code too large to easily use across many CWL’s). I did come up with…

You might be able to modify the solutions there to stage a directory of directories

[mrc]

Hello @matmanc

I am able to reproduce your result; can you open an issue at https://github.com/common-workflow-language/cwltool/issues/new ?

INFO /home/michael/cwltool/env3.9/bin/cwltool 3.0.20210124104916
INFO Resolved 'calibrator.cwl' to 'file:///home/michael/cwltool/calibrator.cwl'
INFO [job test_multiple_dir_input] /tmp/g63y6gd4$ docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/g63y6gd4,target=/EIweox \
    --mount=type=bind,source=/tmp/ajilqq15,target=/tmp \
    --mount=type=bind,source=/home/michael/cwltool/test1,target=/EIweox/test1,readonly \
    --mount=type=bind,source=/home/michael/cwltool/test2,target=/EIweox/test2,readonly \
    --workdir=/EIweox \
    --read-only=true \
    --net=none \
    --log-driver=none \
    --user=1000:1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/EIweox \
    --cidfile=/tmp/px3lec2s/20210305154829-021485.cid \
    lofareosc/prefactor:HBAcalibrator \
    /bin/bash \
    script.sh > /tmp/g63y6gd4/test_multiple_dir_input.log
rm: cannot remove 'test1/dude.txt': Read-only file system
INFO [job test_multiple_dir_input] Max memory used: 0MiB
WARNING [job test_multiple_dir_input] completed permanentFail