From 614cd408c805f036cc4e63bb78b23ce28070e05a Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Tue, 20 Oct 2026 08:40:59 +0200 Subject: [PATCH] Fix check_input nf-test on Nextflow >= 26.10 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. --- nf-tests/check_input.nf.test | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf-tests/check_input.nf.test b/nf-tests/check_input.nf.test index b131a55..f5c690d 100644 --- a/nf-tests/check_input.nf.test +++ b/nf-tests/check_input.nf.test @@ -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") } } }