From 9aff8f9eb93cb536d126ba80a7e2c2317395bc84 Mon Sep 17 00:00:00 2001 From: june-hua Date: Tue, 16 Jun 2026 16:14:44 -0400 Subject: [PATCH 1/2] PHP-160287: Pin nextflow version Nextflow v26 has incompatible config syntax. `wb nextflow` will be deprecated soon, so instead of supporting latest version, use the same nextflow version that workbench uses for workflows created in the UI. PHP-160287 --- features/src/workbench-tools/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/features/src/workbench-tools/install.sh b/features/src/workbench-tools/install.sh index ba5ddbf8..c363e94b 100755 --- a/features/src/workbench-tools/install.sh +++ b/features/src/workbench-tools/install.sh @@ -88,7 +88,7 @@ readonly CONDA_PACKAGES_BINARIES=( "conda-forge::bgenix" "conda-forge::cromwell" "bioconda::ensembl-vep>=115" - "bioconda::nextflow" + "bioconda::nextflow=25.10.02" "bioconda::plink" "bioconda::plink2" "bioconda::regenie" From de540b0ec1683b247f8e63e4fa32f7f69932f935 Mon Sep 17 00:00:00 2001 From: june-hua Date: Tue, 16 Jun 2026 16:23:13 -0400 Subject: [PATCH 2/2] match ver exactly --- features/src/workbench-tools/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/features/src/workbench-tools/install.sh b/features/src/workbench-tools/install.sh index c363e94b..5bab8370 100755 --- a/features/src/workbench-tools/install.sh +++ b/features/src/workbench-tools/install.sh @@ -88,7 +88,7 @@ readonly CONDA_PACKAGES_BINARIES=( "conda-forge::bgenix" "conda-forge::cromwell" "bioconda::ensembl-vep>=115" - "bioconda::nextflow=25.10.02" + "bioconda::nextflow=25.10.2" "bioconda::plink" "bioconda::plink2" "bioconda::regenie"