Adapt for Nextflow 25.10.2 (#68)

* Adapt pipeline for nextflow 25.10.2

* Update dev instructions regarding creating virtual env

* Update PR template

* Update GHAs

Author: matrulda

.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**

.github/workflows/run_tests.yml

@@ -4,36 +4,31 @@ 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
-        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

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

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 ){