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Fix check_input nf-test on Nextflow >= 26.10 #107

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Merged
alpae merged 1 commit into from
Oct 20, 2026
Merged

Fix check_input nf-test on Nextflow >= 26.10 #107

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3 changes: 2 additions & 1 deletion nf-tests/check_input.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,8 @@ nextflow_process {
// fastoma-check-input must reject the mismatch (MYCGE missing from the tree) rather
// than silently pruning or continuing.
assert !process.success
assert process.stdout.any { it.contains("These species are not in the species tree") }
// Nextflow >= 26.10 writes the error report to stderr, older versions to stdout
assert (process.stdout + process.stderr).any { it.contains("These species are not in the species tree") }
}
}

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