From daf4d7b5346bb22799cdd070b865486333816244 Mon Sep 17 00:00:00 2001 From: matrulda Date: Tue, 20 Jan 2026 16:04:54 +0100 Subject: [PATCH 1/4] Adapt pipeline for nextflow 25.10.2 --- .github/workflows/run_tests.yml | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index f1eb519..f0856bf 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -4,7 +4,7 @@ jobs: run-tests: runs-on: ubuntu-22.04 env: - NXF_VER: 21.04.1 + NXF_VER: 25.10.2 NXF_ANSI_LOG: false steps: - name: Check out repository code diff --git a/main.nf b/main.nf index 06f57b4..836f468 100644 --- a/main.nf +++ b/main.nf @@ -234,7 +234,7 @@ process GET_QC_THRESHOLDS { path runfolder output: - path "qc_thresholds.yaml" optional true + path "qc_thresholds.yaml", optional: true script: if ( params.checkqc_config ){ From 33c6c8cf8bcad1beffff2294fb4a62ad56898c67 Mon Sep 17 00:00:00 2001 From: matrulda Date: Tue, 20 Jan 2026 16:05:47 +0100 Subject: [PATCH 2/4] Update dev instructions regarding creating virtual env --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 14b810b..d32789d 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ This is a Nextflow pipeline for generating sequencing reports for the SNP&Se ## Pre-requisites You need to: - install Nextflow (e.g. using conda `conda create -n nextflow-env nextflow` or downloading from [nextflow.io](https://www.nextflow.io/)). - - install [Singularity (version > 2.6)](https://singularity.lbl.gov/install-linux#adding-the-mirror-and-installing). + - install [Apptainer](https://apptainer.org/docs/admin/latest/installation.html). Optional: - (currently mandatory: see known issues) Download the fastq-screen database by downloading fastq-screen from [here](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz), extract the archive and then run `fastq_screen --get_genomes`. @@ -64,11 +64,9 @@ black . Assuming you have installed all pre-requisites (except the fastq screen database: test data comes with a minimal version of it), you can run tests locally by following these steps: ``` -# create virtual environment -virtualenv -p python3.9 venv/ - -# activate venv -source venv/bin/activate +# create a virtual env with a tool of your choice, for example pyenv +pyenv virtualenv 3.11 seqreports +pyenv activate seqreports # install dependencies pip install -r requirements-dev.txt From 3acfb6a23ff01cc85dcb02f042f8fb059cb5531a Mon Sep 17 00:00:00 2001 From: matrulda Date: Tue, 20 Jan 2026 16:10:09 +0100 Subject: [PATCH 3/4] Update PR template --- .github/PULL_REQUEST_TEMPLATE.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6963219..dd8ac7a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,10 +1,7 @@ -**What problems does this PR solve?** -Provide a short description or reference to the relevant issue, explaining what problems this PR solves. +**Description** -**An outline of the validation procedure for this feature** -In addition to automatic tests, has any manual testing been carried out? -**Risk analysis - Reasons for careful code review** -If any of the boxes below are checked, extra careful code review should be inititated. +**Risk analysis** - - [ ] This PR contains code that could remove data + +**Validation procedure** From 84369e8409a61642fa5e8e34ad6d9a6c437ec6b7 Mon Sep 17 00:00:00 2001 From: matrulda Date: Tue, 20 Jan 2026 16:42:16 +0100 Subject: [PATCH 4/4] Update GHAs --- .github/workflows/run_tests.yml | 29 ++++++++++++----------------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index f0856bf..88b3db4 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -8,32 +8,27 @@ jobs: NXF_ANSI_LOG: false steps: - name: Check out repository code - uses: actions/checkout@v2 + uses: actions/checkout@v6 - - name: Cache singularity images - uses: actions/cache@v4.2.2 + - name: Cache singularity/apptainer images + uses: actions/cache@v5.0.2 with: path: work/singularity key: singularity-${{ hashFiles('config/nextflow_config/singularity.config') }} restore-keys: singularity- - - name: Install Singularity - uses: eWaterCycle/setup-singularity@v7 + - name: Install apptainer + uses: eWaterCycle/setup-apptainer@v2 with: - singularity-version: 3.8.3 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - curl -fsSL https://github.com/nextflow-io/nextflow/releases/download/v24.10.4/nextflow -o nextflow | bash - sudo mv nextflow /usr/local/bin/ - - - name: Make Nextflow binary executable - run: chmod +x /usr/local/bin/nextflow + apptainer-version: 1.3.6 + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: 25.10.2 + - name: Set up python - uses: actions/setup-python@v2 + uses: actions/setup-python@v6 with: python-version: 3.11 architecture: x64