Repository navigation
Fix check_input nf-test on Nextflow >= 26.10 - #107
Merged
Merged
Conversation
Nextflow 26.10 writes the error report to stderr instead of stdout, so the assertion looking for the species-tree mismatch message only in stdout failed on the latest-everything CI matrix. Search both streams.
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
The
processtests on thelatest-everythingCI matrix (all profiles) have been failing since Nextflow 26.10 became the latest release.The
check_inputfailure-case test correctly fails, but its assertion only searchedprocess.stdoutfor the error message. Nextflow 26.10 reports process errors on stderr (24.10.2 and 26.09 used stdout), so the message was no longer found. The assertion now searches both streams, which works for old and new Nextflow versions.