Merge branch 'dev' into nf-core-template-merge-3.0.2

nf-core · Oct 17, 2024 · 1832c00 · 1832c00
2 parents 75e75af + c293787
commit 1832c00
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -17,6 +17,10 @@ jobs:
     # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
     if: github.repository == 'nf-core/viralrecon' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
+    # Do a full-scale run with data from each sequencing platform
+    strategy:
+      matrix:
+        platform: ["illumina", "nanopore"]
     steps:
       - uses: octokit/[email protected]
         id: check_approvals
@@ -32,9 +36,6 @@ jobs:
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         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: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -44,10 +45,9 @@ jobs:
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}"
             }
-          profiles: test_full
-
+          profiles: test_full_${{ matrix.platform }},aws_tower
       - uses: actions/upload-artifact@v4
         with:
           name: Seqera Platform debug log file

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -83,3 +83,236 @@ jobs:
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+
+  test_parameters:
+    name: "Test parameters (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        parameters:
+          - "--consensus_caller ivar"
+          - "--variant_caller bcftools --consensus_caller ivar"
+          - "--skip_fastp --skip_pangolin"
+          - "--skip_variants"
+          - "--skip_cutadapt --skip_snpeff"
+          - "--skip_kraken2"
+          - "--skip_assembly"
+          - "--spades_mode corona"
+          - "--spades_mode metaviral"
+          - "--skip_plasmidid false --skip_asciigenome"
+          - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz"
+          - "--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Download GTF for additional annotation
+        if: contains(matrix.parameters, 'additional_annotation')
+        run: |
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz
+
+      - name: Download prebuild bowtie2 index
+        if: contains(matrix.parameters, 'bowtie2_index')
+        run: |
+          wget https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz
+
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}"
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results
+
+  test_sispa:
+    name: "Test SISPA (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        parameters:
+          - "--gff false"
+          - "--genome 'NC_045512.2'"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}"
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results
+
+  test_nanopore:
+    name: "Test nanopore (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        parameters:
+          - "--gff false --freyja_depthcutoff 1"
+          - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1"
+          - "--input false --freyja_depthcutoff 1"
+          - "--min_barcode_reads 10000"
+          - "--min_guppyplex_reads 10000"
+          - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1"
+          - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Download GTF for additional annotation
+        if: contains(matrix.parameters, 'additional_annotation')
+        run: |
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz
+
+      - name: Download medaka model
+        if: contains(matrix.parameters, 'r941_min_high_g360_model.hdf5')
+        run: |
+          wget https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g360_model.hdf5
+
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}"
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -14,6 +14,7 @@ template:
   name: viralrecon
   org: nf-core
   outdir: .
-  skip_features: null
+  skip_features:
+    - igenomes
   version: 2.7.0dev
 update: null