Release 0.4.0

.editorconfig

@@ -31,8 +31,3 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
-
-# ignore parameters.md
-[parameters.md]
-trim_trailing_whitespace = false
-indent_style = unset

.github/CONTRIBUTING.md

@@ -16,7 +16,7 @@ If you'd like to write some code for genomic-medicine-sweden/nallo, the standard
 1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/nallo issues](https://github.com/genomic-medicine-sweden/nallo/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [genomic-medicine-sweden/nallo repository](https://github.com/genomic-medicine-sweden/nallo) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -36,14 +36,14 @@ There are typically two types of tests that run:
 
 ### Lint tests
 
-Altough this is not a `nf-core` pipeline, `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all their pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, they have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+Although this is not a `nf-core` pipeline, `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all their pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, they have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline tests
 
-This pipeline should be set up with a minimal set of test-data.
+This pipeline is set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
@@ -68,22 +68,23 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+10. Update the tool references `assets/software_references.yml`.
+11. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -96,7 +97,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,46 +9,34 @@ body:
       description: A clear and concise description of what the bug is.
     validations:
       required: true
+
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used
-        to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: "$ nextflow run ...
-
+      placeholder: |
+        $ nextflow run ...
 
         Some output where something broke
 
-        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: "Please drag and drop the relevant files here. Create a `.zip` archive
-        if the extension is not allowed.
-
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-        in the directory where you launched the pipeline)_ as well as custom Nextflow
-        configuration files.
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
 
-        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: "* Nextflow version _(eg. 23.04.0)_
-
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
-
         * Executor _(eg. slurm, local, awsbatch)_
-
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-        or Apptainer)_
-
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
         * Version of genomic-medicine-sweden/nallo _(eg. 1.1, 1.5, 1.8.2)_
-
-        "

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medi
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/nallo/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/build-docs.yml

@@ -0,0 +1,43 @@
+name: build docs
+# https://github.com/nf-cmgg/structural/blob/master/.github/workflows/build-docs.yml
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - name: Obtain version from nextflow config
+        run: |
+          version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)
+          [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version
+          echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
+      - name: Setup git user
+        run: |
+          git config --global user.name "${{github.actor}}"
+          git config --global user.email "${{github.actor}}@users.noreply.github.com"
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - name: Install dependencies
+        run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
+      - name: Build docs
+        run: |
+          [[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} || mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+      - name: Set default docs
+        run: mike set-default --push latest

.github/workflows/ci.yml

@@ -7,9 +7,13 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NFTEST_VER: "0.9.2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -20,88 +24,55 @@ permissions:
 
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - ""
-          - "--preset ONT_R10 --input https://github.com/genomic-medicine-sweden/test-datasets/raw/e2266a34c14d1e0a9ef798de3cd81a76c9216fc1/testdata/samplesheet_multisample_bam_ont.csv --parallel_alignments 2 --parallel_snv 1"
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-  nftest:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: ${{ matrix.tags }} | ${{ matrix.profile }} | NF-${{ matrix.NXF_VER }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
+          - "24.04.2"
           - "latest-everything"
-          - "23.04.0"
         tags:
-          - "SHORT_VARIANT_CALLING"
-          - "SNV_ANNOTATION"
           - "samplesheet"
           - "samplesheet_multisample_bam"
+          - "samplesheet_multisample_ont_bam"
+          - "SHORT_VARIANT_CALLING"
+          - "SNV_ANNOTATION"
+          - "CALL_SVS"
+          - "ANNOTATE_SVS"
+          - "RANK_VARIANTS"
+          - "CALL_REPEAT_EXPANSIONS"
+          - "METHYLATION"
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        with:
+          fetch-depth: 0
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
       - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
+          install-pdiff: true
 
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
           architecture: "x64"
 
-      - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always() # always run even if the previous step fails
-        with:
-          report_paths: test.xml
+          nf-test test \
+            --ci \
+            --changed-since HEAD^ \
+            --verbose \
+            --tag ${{ matrix.tags }} \
+            --profile "+${{ matrix.profile }}" \
+            --junitxml=test.xml

.github/workflows/ci_master.yml

@@ -39,7 +39,7 @@ jobs:
         parameters:
           - "--bed=`null`"
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: Check out pipeline code