Fixed output step when it is an empty list#472
Merged
GlassOfWhiskey merged 1 commit intomasterfrom Jun 6, 2024
Merged
Conversation
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #472 +/- ##
=======================================
Coverage 70.24% 70.24%
=======================================
Files 85 85
Lines 10642 10642
Branches 2505 2505
=======================================
Hits 7475 7475
- Misses 2703 2709 +6
+ Partials 464 458 -6 ☔ View full report in Codecov by Sentry. |
LanderOtto
added a commit
that referenced
this pull request
Mar 11, 2026
…en an output was mandatory but the glob found no files, an empty token was propagated. Now, if no files match: a list is propagated for mandatory outputs, while an empty token is propagated for optional outputs. Moreover, this commit streamlines command output processing by removing the manual manipulation of glob results and instead leveraging the single logic already present. This same issue with empty globs was previously solved in #472; a regression test has now been added to prevent future occurrences.
Merged
GlassOfWhiskey
pushed a commit
that referenced
this pull request
Mar 13, 2026
This commit fixes an issue introduced in #959. Before this commit, when an output was a mandatory list of files but the glob found no files, an empty token was propagated. Now, if no files match: a list is propagated for mandatory outputs, while an empty token is propagated for optional outputs. Moreover, this commit streamlines command output processing by removing the manual manipulation of glob results and instead leveraging the `single` logic already present in the `CWLCommandOutputProcessor`. This same issue with empty globs was previously solved in #472; a regression test has now been added to prevent future occurrences.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This commit returns an empty list when no data are generated from a CWL step that expects an
arrayoutput type. In addition, this commit forces all output processors to beoptionalwhen anarrayoutput type is specified, as the CWL standard allows falling back to an empty list even for non-optional output parameters.