Fix changelog.

.devcontainer/devcontainer.json

@@ -10,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/fetc
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fetchngs/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/fetchngs _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/include.yaml

@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

.github/workflows/ci.yml

@@ -27,89 +27,45 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      changes: ${{ steps.changed_files.outputs.any_modified }}
-      tags: ${{ steps.list.outputs.tags }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - uses: tj-actions/changed-files@v42
-        id: changed_files
-        with:
-          dir_names: "true"
-          output_renamed_files_as_deleted_and_added: "true"
-          # Define list of additional rules for testing paths
-          # Mostly, we define additional 'pipeline' or 'all' tests here
-          files_yaml: |
-            ".":
-              - .github/workflows/**
-              - nf-test.config
-              - nextflow.config
-            tests:
-              - assets/*
-              - bin/*
-              - conf/*
-              - main.nf
-              - nextflow_schema.json
-
-          files_ignore: |
-            .git*
-            .gitpod.yml
-            .prettierignore
-            .prettierrc.yml
-            **.md
-            **.png
-            modules.json
-            pyproject.toml
-            tower.yml
-
-      - name: debug
-        run: |
-          echo ${{ steps.changed_files.outputs.any_modified }}
-          echo ${{ steps.changed_files.outputs.all_changed_files }}
-          echo ${{ steps.changed_files.outputs.changed_keys }}
-
-      - name: nf-test list tags
+      - name: List nf-test files
         id: list
-        if: ${{ steps.changed_files.outputs.any_modified }}
-        run: |
-          echo tags=$(python \
-            .github/python/find_changed_files.py \
-            -t pipeline workflow process \
-            -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
-          ) >> $GITHUB_OUTPUT
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.3
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
 
-      - name: debug2
+      - name: print list of nf-test files
         run: |
-          echo ${{ steps.list.outputs.tags }}
+          echo ${{ steps.list.outputs.components }}
 
   test:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes]
-    if: needs.changes.outputs.changes
+    if: needs.changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
           - "latest-everything"
           - "23.04"
-        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -140,7 +96,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:

.github/workflows/download_pipeline.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.github/workflows/release-announcements.yml

@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:

.gitpod.yml

@@ -10,13 +10,11 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [PR #299](https://github.com/nf-core/fetchngs/pull/299) - Template update for nf-core/tools v2.13.1
+- [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
+- [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
+- [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
 - [PR #319](https://github.com/nf-core/fetchngs/pull/319) - Update subworkflows and modules to be TES compliance.
 
 ### :warning: Major enhancements
@@ -15,11 +19,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add support for tags
 - Updated `multiqc_mappings_config` to have different matching pattern for `config.yml` vs `versions.yml`
 
-### Credits
 
-Special thanks to the following for their contributions to the release:
+### Software dependencies
 
-- [Venkat Malladi](https://github.com/vsmalladi)
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `wget`     | 1.20.1      | 1.21.4      |
+| `sratools` | 3.0.8       | 3.1.0       |
 
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 

modules/local/sra_fastq_ftp/main.nf

@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda "conda-forge::wget=1.20.1"
+    conda "conda-forge::wget=1.21.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
-        'biocontainers/wget:1.20.1' }"
+        'https://depot.galaxyproject.org/singularity/wget:1.21.4' :
+        'biocontainers/wget:1.21.4' }"
 
     input:
     tuple val(meta), val(fastq)