From df0ec8bf0d8689bc694bba34bbb7b6aac3d371d4 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 2 Jul 2025 16:35:43 +0200 Subject: [PATCH 1/2] Fix collectFile cache issue causing software version inconsistencies MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add cache: false to collectFile() call for software versions collection to prevent inconsistencies when using Nextflow resume function. When collectFile uses storeDir with caching enabled, it can lead to missing or additional processes in software version reports across multiple pipeline runs with resume. Fixes #3653 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/pipeline-template/workflows/pipeline.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 6126f9ec69..06c7f58cd9 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -55,7 +55,8 @@ workflow {{ short_name|upper }} { storeDir: "${params.outdir}/pipeline_info", name: {% if is_nfcore %}'nf_core_' + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml', sort: true, - newLine: true + newLine: true, + cache: false ).set { ch_collated_versions } {% if multiqc %} From 531be4b66d0d0dc0fa87d9fcaf56e108a0fedc3b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 2 Jul 2025 14:40:53 +0000 Subject: [PATCH 2/2] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 577c8ed101..96a41dcb00 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ - Update gitpod/workspace-base Docker digest to 77021d8 ([#3649](https://github.com/nf-core/tools/pull/3649)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.1 ([#3648](https://github.com/nf-core/tools/pull/3648)) - Update error message for rocrate_readme_sync ([#3652](https://github.com/nf-core/tools/pull/3652)) +- Fix collectFile cache issue causing software version inconsistencies ([#3654](https://github.com/nf-core/tools/pull/3654)) ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]