Merge branch 'nf-core-template-merge-2.9' into dev

# Conflicts: # README.md # assets/multiqc_config.yml # bin/check_samplesheet.py # conf/base.config # modules.json # modules/nf-core/bcftools/sort/main.nf # modules/nf-core/bcftools/sort/meta.yml # modules/nf-core/bcftools/stats/main.nf # modules/nf-core/bcftools/stats/meta.yml # modules/nf-core/bwa/index/main.nf # modules/nf-core/bwa/index/meta.yml # modules/nf-core/bwa/mem/main.nf # modules/nf-core/bwa/mem/meta.yml # modules/nf-core/bwamem2/index/main.nf # modules/nf-core/bwamem2/index/meta.yml # modules/nf-core/bwamem2/mem/main.nf # modules/nf-core/bwamem2/mem/meta.yml # modules/nf-core/cat/cat/main.nf # modules/nf-core/cat/cat/meta.yml # modules/nf-core/cat/fastq/main.nf # modules/nf-core/cat/fastq/meta.yml # modules/nf-core/custom/dumpsoftwareversions/main.nf # modules/nf-core/dragmap/align/main.nf # modules/nf-core/dragmap/align/meta.yml # modules/nf-core/dragmap/hashtable/main.nf # modules/nf-core/dragmap/hashtable/meta.yml # modules/nf-core/ensemblvep/Dockerfile # modules/nf-core/ensemblvep/build.sh # modules/nf-core/ensemblvep/environment.yml # modules/nf-core/ensemblvep/main.nf # modules/nf-core/ensemblvep/meta.yml # modules/nf-core/fastp/main.nf # modules/nf-core/fastp/meta.yml # modules/nf-core/fgbio/callmolecularconsensusreads/main.nf # modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml # modules/nf-core/fgbio/fastqtobam/main.nf # modules/nf-core/fgbio/fastqtobam/meta.yml # modules/nf-core/fgbio/groupreadsbyumi/main.nf # modules/nf-core/fgbio/groupreadsbyumi/meta.yml # modules/nf-core/freebayes/main.nf # modules/nf-core/freebayes/meta.yml # modules/nf-core/gatk4/applybqsr/main.nf # modules/nf-core/gatk4/applybqsr/meta.yml # modules/nf-core/gatk4/applybqsrspark/main.nf # modules/nf-core/gatk4/applybqsrspark/meta.yml # modules/nf-core/gatk4/applyvqsr/main.nf # modules/nf-core/gatk4/applyvqsr/meta.yml # modules/nf-core/gatk4/baserecalibrator/main.nf # modules/nf-core/gatk4/baserecalibrator/meta.yml # modules/nf-core/gatk4/baserecalibratorspark/main.nf # modules/nf-core/gatk4/baserecalibratorspark/meta.yml # modules/nf-core/gatk4/bedtointervallist/main.nf # modules/nf-core/gatk4/bedtointervallist/meta.yml # modules/nf-core/gatk4/calculatecontamination/main.nf # modules/nf-core/gatk4/calculatecontamination/meta.yml # modules/nf-core/gatk4/createsequencedictionary/main.nf # modules/nf-core/gatk4/createsequencedictionary/meta.yml # modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf # modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml # modules/nf-core/gatk4/filtermutectcalls/main.nf # modules/nf-core/gatk4/filtermutectcalls/meta.yml # modules/nf-core/gatk4/filtersamreads/main.nf # modules/nf-core/gatk4/filtersamreads/meta.yml # modules/nf-core/gatk4/filtervarianttranches/main.nf # modules/nf-core/gatk4/filtervarianttranches/meta.yml # modules/nf-core/gatk4/gatherbqsrreports/main.nf # modules/nf-core/gatk4/gatherbqsrreports/meta.yml # modules/nf-core/gatk4/gatherpileupsummaries/main.nf # modules/nf-core/gatk4/gatherpileupsummaries/meta.yml # modules/nf-core/gatk4/genomicsdbimport/main.nf # modules/nf-core/gatk4/genomicsdbimport/meta.yml # modules/nf-core/gatk4/genotypegvcfs/main.nf # modules/nf-core/gatk4/genotypegvcfs/meta.yml # modules/nf-core/gatk4/getpileupsummaries/main.nf # modules/nf-core/gatk4/getpileupsummaries/meta.yml # modules/nf-core/gatk4/haplotypecaller/main.nf # modules/nf-core/gatk4/haplotypecaller/meta.yml # modules/nf-core/gatk4/indexfeaturefile/main.nf # modules/nf-core/gatk4/indexfeaturefile/meta.yml # modules/nf-core/gatk4/intervallisttobed/main.nf # modules/nf-core/gatk4/intervallisttobed/meta.yml # modules/nf-core/gatk4/intervallisttools/main.nf # modules/nf-core/gatk4/intervallisttools/meta.yml # modules/nf-core/gatk4/learnreadorientationmodel/main.nf # modules/nf-core/gatk4/learnreadorientationmodel/meta.yml # modules/nf-core/gatk4/markduplicates/main.nf # modules/nf-core/gatk4/markduplicates/meta.yml # modules/nf-core/gatk4/markduplicatesspark/main.nf # modules/nf-core/gatk4/markduplicatesspark/meta.yml # modules/nf-core/gatk4/mergemutectstats/main.nf # modules/nf-core/gatk4/mergemutectstats/meta.yml # modules/nf-core/gatk4/mergevcfs/main.nf # modules/nf-core/gatk4/mergevcfs/meta.yml # modules/nf-core/gatk4/mutect2/main.nf # modules/nf-core/gatk4/mutect2/meta.yml # modules/nf-core/gatk4/splitncigarreads/main.nf # modules/nf-core/gatk4/splitncigarreads/meta.yml # modules/nf-core/gatk4/variantfiltration/main.nf # modules/nf-core/gatk4/variantfiltration/meta.yml # modules/nf-core/gatk4/variantrecalibrator/main.nf # modules/nf-core/gatk4/variantrecalibrator/meta.yml # modules/nf-core/gffread/main.nf # modules/nf-core/gffread/meta.yml # modules/nf-core/gunzip/main.nf # modules/nf-core/gunzip/meta.yml # modules/nf-core/hisat2/align/main.nf # modules/nf-core/hisat2/align/meta.yml # modules/nf-core/hisat2/build/main.nf # modules/nf-core/hisat2/build/meta.yml # modules/nf-core/hisat2/extractsplicesites/main.nf # modules/nf-core/hisat2/extractsplicesites/meta.yml # modules/nf-core/manta/germline/main.nf # modules/nf-core/manta/germline/meta.yml # modules/nf-core/manta/somatic/main.nf # modules/nf-core/manta/somatic/meta.yml # modules/nf-core/manta/tumoronly/main.nf # modules/nf-core/manta/tumoronly/meta.yml # modules/nf-core/modules/fastqc/main.nf # modules/nf-core/modules/multiqc/main.nf # modules/nf-core/mosdepth/main.nf # modules/nf-core/mosdepth/meta.yml # modules/nf-core/multiqc/meta.yml # modules/nf-core/sage/main.nf # modules/nf-core/sage/meta.yml # modules/nf-core/samblaster/main.nf # modules/nf-core/samblaster/meta.yml # modules/nf-core/samtools/bam2fq/main.nf # modules/nf-core/samtools/bam2fq/meta.yml # modules/nf-core/samtools/collatefastq/main.nf # modules/nf-core/samtools/collatefastq/meta.yml # modules/nf-core/samtools/convert/main.nf # modules/nf-core/samtools/convert/meta.yml # modules/nf-core/samtools/faidx/main.nf # modules/nf-core/samtools/faidx/meta.yml # modules/nf-core/samtools/flagstat/main.nf # modules/nf-core/samtools/flagstat/meta.yml # modules/nf-core/samtools/idxstats/main.nf # modules/nf-core/samtools/idxstats/meta.yml # modules/nf-core/samtools/index/main.nf # modules/nf-core/samtools/index/meta.yml # modules/nf-core/samtools/merge/main.nf # modules/nf-core/samtools/merge/meta.yml # modules/nf-core/samtools/mpileup/main.nf # modules/nf-core/samtools/mpileup/meta.yml # modules/nf-core/samtools/sort/main.nf # modules/nf-core/samtools/sort/meta.yml # modules/nf-core/samtools/stats/main.nf # modules/nf-core/samtools/stats/meta.yml # modules/nf-core/samtools/view/main.nf # modules/nf-core/samtools/view/meta.yml # modules/nf-core/snpeff/Dockerfile # modules/nf-core/snpeff/build.sh # modules/nf-core/snpeff/environment.yml # modules/nf-core/snpeff/main.nf # modules/nf-core/snpeff/meta.yml # modules/nf-core/star/align/main.nf # modules/nf-core/star/align/meta.yml # modules/nf-core/star/genomegenerate/main.nf # modules/nf-core/star/genomegenerate/meta.yml # modules/nf-core/strelka/germline/main.nf # modules/nf-core/strelka/germline/meta.yml # modules/nf-core/strelka/somatic/main.nf # modules/nf-core/strelka/somatic/meta.yml # modules/nf-core/tabix/bgziptabix/main.nf # modules/nf-core/tabix/bgziptabix/meta.yml # modules/nf-core/tabix/tabix/main.nf # modules/nf-core/tabix/tabix/meta.yml # modules/nf-core/untar/main.nf # modules/nf-core/untar/meta.yml # modules/nf-core/unzip/main.nf # modules/nf-core/unzip/meta.yml # modules/nf-core/vcflib/filter/main.nf # modules/nf-core/vcflib/filter/meta.yml # modules/nf-core/vcftools/main.nf # modules/nf-core/vcftools/meta.yml # nextflow.config # workflows/rnadnavar.nf
nrhorner · Aug 16, 2023 · 87e5339 · 87e5339
2 parents e7b43bb + 5cd65a2
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "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"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.gitattributes b/.gitattributes
@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -101,3 +101,18 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/rnadnavar/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,9 +42,9 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * 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 or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/rnadnavar _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnad
 
 - [ ] 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/nf-core/rnadnavar/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/rnadnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnadnavar/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/rnadnavar _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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -14,17 +14,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadnavar/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadnavar/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -12,14 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnadnavar/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnadnavar/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/rnadnavar'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnadnavar ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnadnavar ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -10,7 +10,10 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
 
 jobs:
   test:
@@ -20,27 +23,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required

diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,32 +27,58 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
 
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
-          python-version: "3.6"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies
@@ -71,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier
diff --git a/.prettierignore b/.prettierignore
@@ -1,4 +1,6 @@
 email_template.html
+adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -7,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -12,7 +12,10 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
@@ -31,5 +34,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.