From 6cec83ee3e3d6f2c58e012f6d6240f04c985be18 Mon Sep 17 00:00:00 2001 From: Samarth Mathur Date: Tue, 3 Jun 2025 13:12:30 -0400 Subject: [PATCH 1/3] fix: load nextflow v25 resolves #70 --- src/__main__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/__main__.py b/src/__main__.py index ca00096..fafc9e1 100644 --- a/src/__main__.py +++ b/src/__main__.py @@ -141,6 +141,7 @@ def run(main_path, output, _mode, force_all, **kwargs): mode=_mode, force_all=force_all, pipeline_name="LOGAN", + hpc_modules="nextflow/25", **kwargs, ) finally: From 4a6826a9a1ddc91211f81931c6239b33bbdbf77d Mon Sep 17 00:00:00 2001 From: Samarth Mathur Date: Tue, 3 Jun 2025 13:15:47 -0400 Subject: [PATCH 2/3] chore: Update CHANGELOG.md --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3defcfb..d13bd31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,6 @@ ## LOGAN development version - +- Uses Nextflow v25 for logan run (#99, @samarth8392) +- ## LOGAN 0.3.1 - Improve help message for `logan run`. (#97, @kelly-sovacool) From 5f416821b102a426a8db50d5f8617937ad3f12f1 Mon Sep 17 00:00:00 2001 From: Samarth Mathur Date: Tue, 3 Jun 2025 13:21:57 -0400 Subject: [PATCH 3/3] chore: Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d13bd31..5402276 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,5 @@ ## LOGAN development version -- Uses Nextflow v25 for logan run (#99, @samarth8392) +- Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: https://github.com/nextflow-io/nextflow/issues/5456) (#99, @samarth8392) - ## LOGAN 0.3.1