Renku complains about outputs of un-executed workflow file steps

[m-alisafaee]

When executing a subset of step from a workflow file, Renku will complain the outputs of the un-executed steps cannot be found.

To reproduce:

1. Create a project
2. Unzip and copy the attached workflow file to the project: workflow-file.yml.zip
3. renku run workflow-file.yml head tail

Executing step 'workflow-file.head': 'head -n10 Dockerfile > intermediate' ...
Executing step 'workflow-file.tail': 'tail -n5 intermediate > results/output.csv' ...
Error: Git command failed: Cmd('git') failed due to: exit code(1)
  cmdline: git commit --message=renku run workflow-file.yml head tail

renku-transaction: d37de79845544734b296883470fbc9a1 --no-verify -- workflow-file.yml Dockerfile intermediate results/output.csv results/output.csv results/output.csv.wc /private/tmp/workflow-file-bug/.renku
  stderr: 'error: pathspec 'results/output.csv.wc' did not match any file(s) known to git'

Traceback (most recent call last):
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/infrastructure/repository.py", line 1780, in _run_git_command
    return getattr(repository.git, command)(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/git/cmd.py", line 639, in <lambda>
    return lambda *args, **kwargs: self._call_process(name, *args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/git/cmd.py", line 1184, in _call_process
    return self.execute(call, **exec_kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/git/cmd.py", line 984, in execute
    raise GitCommandError(redacted_command, status, stderr_value, stdout_value)
git.exc.GitCommandError: Cmd('git') failed due to: exit code(1)
  cmdline: git commit --message=renku run workflow-file.yml head tail

renku-transaction: d37de79845544734b296883470fbc9a1 --no-verify -- workflow-file.yml Dockerfile intermediate results/output.csv results/output.csv results/output.csv.wc /private/tmp/workflow-file-bug/.renku
  stderr: 'error: pathspec 'results/output.csv.wc' did not match any file(s) known to git'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/ui/cli/exception_handler.py", line 92, in main
    return super().main(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/ui/cli/run.py", line 612, in run
    run_workflow_file_command(no_commit=no_commit, commit_only=commit_only)
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/command/command_builder/command.py", line 266, in execute
    hook(self, context, result, *args, **kwargs)
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/command/command_builder/command.py", line 202, in _post_hook
    raise result.error
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/command/command_builder/repo.py", line 96, in _post_hook
    finalize_commit(
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/core/util/git.py", line 1127, in finalize_commit
    repository.commit(commit_message + transaction_id, committer=committer, no_verify=True, paths=paths)
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/infrastructure/repository.py", line 263, in commit
    self.run_git_command(
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/infrastructure/repository.py", line 406, in run_git_command
    return _run_git_command(self._repository, command, *args, **kwargs)
  File "/Users/Mohammad/Documents/Workspace.noindex/sdsc/code/renku-python/renku/infrastructure/repository.py", line 1782, in _run_git_command
    raise errors.GitCommandError(
renku.core.errors.GitCommandError: Git command failed: Cmd('git') failed due to: exit code(1)
  cmdline: git commit --message=renku run workflow-file.yml head tail

renku-transaction: d37de79845544734b296883470fbc9a1 --no-verify -- workflow-file.yml Dockerfile intermediate results/output.csv results/output.csv results/output.csv.wc /private/tmp/workflow-file-bug/.renku
  stderr: 'error: pathspec 'results/output.csv.wc' did not match any file(s) known to git'