0.1.6: can't run montage workflow `KeyError: '/band/run/wdiff/run/in/band_id'`

[mr-c]

Workflow:
https://github.com/alpha-unito/cwl-montage-workflow/tree/df569e5805a8c7c547b786244d5463f6b63dd703

invocation: TMPDIR=/srv/public/crusoe/tmp_streamflow cwl-runner --outdir /srv/public/crusoe/results_streamflow cwl/main_montage.cwl data/config_montage.json

(data was previously download with cwltool)

streamflow_log.txt

[mr-c]

Okay, some progess, now with installing the latest version from this repo: ERROR [Errno 13] Permission denied: '/public'

invocation: TMPDIR=/srv/public/crusoe/tmp_streamflow streamflow run streamflow.yml --outdir /srv/public/crusoe/results_streamflow

streamflow.yml

version: v1.0
workflows:
  main:
    type: cwl
    config:
      file: cwl/main_montage.cwl
      settings: data/config_montage.json
      docker:
        - step: /
          deployment:
            type: singularity
            config: {}

log:

streamflow_20251210_log.txt

[LanderOtto]

Could you test PR #894 to see if it resolves your issue?

[mr-c]

Hello @LanderOtto ; with #894 I'm still getting the errors about trying to create /public/crusoe/tmp_streamflow/streamflow/d6d6f0cc-bb16-40d9-8dd6-9950960a8601

$TMPDIR is /srv/public/crusoe/tmp_streamflow not /public/crusoe/tmp_streamflow ..

[LanderOtto]

Could you please execute the readlink -f /srv/public/crusoe/tmp_streamflow command? Just to verify that /public/crusoe/tmp_streamflow is not the real path.

Moreover, could you provide the log of the execution using the PR and the flag --debug?

[mr-c]

$ readlink -f /srv/public/crusoe/tmp_streamflow
/srv/public/crusoe/tmp_streamflow
$ readlink -f /srv/public/crusoe/tmp_streamflow2
/srv/public/crusoe/tmp_streamflow2

Here is the full log: (this time I ran using the in-memory database as I have another streamflow execution running and the default database was locked; the error is the same)

streamflow2_log.txt