miniwdl run using inputs (-i) "File not found"

[rpetit3]

Hello!

I'm really hoping this is just a simple issue and can be resolved as just "user error". But here's the deal I have a workflow that runs fine with Cromwell, but with MiniWDL, I get a "File not found:" error, with no real indication of which file was not found.

# Cromwell
cromwell run ~/repos/public_health_viral_genomics/workflows/wf_titan_gc.wdl --inputs samples.json -m metadata.json
... does its thing and finishes successfully ...

# MiniWDL
 miniwdl run /home/robert_petit/repos/public_health_viral_genomics/workflows/wf_titan_gc.wdl -i /home/robert_petit/test/titan/samples.json -v
2021-06-28 22:24:06.065 miniwdl-run read configuration file :: path: "/home/robert_petit/.config/miniwdl.cfg"

File not found:

Here's the JSON file (samples.json)

{
    "titan_gc.samples": [
        {
            "samplename": "clearlabs_sample",
            "run_id": "clearlabs_test",
            "platform": "clearlabs",
            "r1": "/home/robert_petit/test/titan/clearlabs.fastq.gz",
            "r2": "",
            "primer_bed": "/home/robert_petit/test/titan/artic_V3_nCoV-2019.bed"
        }
    ]
}

Each of the expected inputs exists:

ls -lh /home/robert_petit/test/titan/clearlabs.fastq.gz
-rw-r--r-- 1 robert_petit robert_petit 4.1M Jun 28 22:26 /home/robert_petit/test/titan/clearlabs.fastq.gz

ls -lh /home/robert_petit/test/titan/artic_V3_nCoV-2019.bed
-rw-r--r-- 56 robert_petit robert_petit 9.7K Jun 18 05:34 /home/robert_petit/test/titan/artic_V3_nCoV-2019.bed

ls -lh /home/robert_petit/repos/public_health_viral_genomics/workflows/wf_titan_gc.wdl
-rw-r--r-- 1 robert_petit robert_petit 21K Jun 24 14:07 /home/robert_petit/repos/public_health_viral_genomics/workflows/wf_titan_gc.wdl

ls -lh /home/robert_petit/test/titan/samples.json
-rw-r--r-- 1 robert_petit robert_petit 1.5K Jun 24 14:09 /home/robert_petit/test/titan/samples.json

System Details (using conda versions)

lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 10 (buster)
Release:        10
Codename:       buster

miniwdl --version
miniwdl v1.2.0

cromwell --version
cromwell 64

Please let me know if I can provide more details, or there is anything you would like me to try. (even better if its just user error and a simple change is needed)

Thank you!

[mlin]

My suspicion lands squarely here:

            "r2": "",

If r2 is a File? input, can you try deleting that line and see if it then works with miniwdl? (If so, I can then start a discussion with OpenWDL and/or Cromwell on how we should interpret an empty-string input there)

[rpetit3]

@mlin that was the issue (trying to open empty string). I can work with this thank you very much!