include MiXCR toolkit in nf-core/airrflow

.github/workflows/ci.yml

@@ -104,6 +104,8 @@ jobs:
             "test_assembled_hs",
             "test_assembled_mm",
             "test_10x_sc",
+            "test_mixcr_bulk",
+            "test_mixcr_sc",
             "test_clontech_umi",
             "test_nebnext_umi",
             "test_rnaseq_bulk",
@@ -135,3 +137,52 @@ jobs:
             /home/runner/work
             !/home/runner/work/conda
             !/home/runner/work/singularity
+  test_profile_download:
+    name: nf-test with profiles needing mixcr license
+    # Only run on PRs from branches of nf-core/airrflow repository or on push if this is the nf-core dev branch (merged PRs)
+    # (GitHub secrets are not accessible for workflows from forks!)
+    if: "${{ github.event.pull_request.head.repo.full_name == 'nf-core/airrflow' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+        profile: ["test_mixcr_bulk", "test_mixcr_sc"]
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - name: Run nf-test
+        env:
+          NCBI_EMAIL: ${{ secrets.MIXCR_LICENSE }}
+        run: |
+          nextflow secrets set MIXCR_LICENSE ${{ secrets.MIXCR_LICENSE }}
+          nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml --verbose
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "*.xml"

conf/modules.config

@@ -731,4 +731,40 @@ process {
         ]
     }
 
+    // -------------------------------
+    // MiXCR
+    // -------------------------------
+
+    withName: MIXCR_IND_POSTANALYSIS {
+        publishDir = [
+            path: { "${params.outdir}/mixcr/individual_postanalysis" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MIXCR_IND_PLOTS {
+        publishDir = [
+            path: { "${params.outdir}/mixcr/individual_postanalysis/plots" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MIXCR_OVERLAP_POSTANALYSIS {
+        publishDir = [
+            path: { "${params.outdir}/mixcr/overlap_postanalysis" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MIXCR_OVERLAP_PLOTS {
+        publishDir = [
+            path: { "${params.outdir}/mixcr/overlap_postanalysis/plots" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }

conf/test_mixcr_bulk.config

@@ -0,0 +1,40 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/airrflow -profile test_mixcr_bulk,<docker/singularity>
+ */
+
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name = 'Test MiXCR toolset on bulk data.'
+    config_profile_description = 'Minimal test dataset to check pipeline functionality with raw bulk data using the MiXCR toolset'
+
+
+    // params
+    mode = 'fastq'
+    library_generation_method = 'mixcr'
+    kit = "irepertoire-human-rna-xcr-repseq-lr"
+    clonal_threshold = 0
+    mixcr_postanalysis = true
+    mixcr_downsampling = "count-read-auto"
+    mixcr_weightfunction = "none"
+    mixcr_productive_only = true
+    mixcr_drop_outliers = true
+    mixcr_overlap_criteria = "CDR3|AA|V|J"
+    mixcr_diversity_plottype = "boxplot"
+
+
+    // Input data
+    input = pipelines_testdata_base_path + 'testdata-tcr/TCR_metadata_airr.tsv'
+    imgt_mixcr = "https://github.com/repseqio/library-imgt/releases/download/v8/imgt.202312-3.sv8.json.gz"
+}

conf/test_mixcr_sc.config

@@ -0,0 +1,42 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/airrflow -profile test_mixcr_sc,<docker/singularity>
+ */
+
+includeConfig "https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-mixcr/10x_sc.conf"
+
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name = 'Test MiXCR sc analysis.'
+    config_profile_description = 'Minimal test dataset to check pipeline functionality with raw single cell data from 10xGenomics using the MiXCR toolset'
+
+    // params
+    mode = 'fastq'
+    library_generation_method = 'mixcr'
+    clonal_threshold = 0
+    kit = '10x-sc-xcr-vdj'
+    mixcr_postanalysis = true
+    mixcr_downsampling = "count-read-auto"
+    mixcr_weightfunction = "none"
+    mixcr_productive_only = true
+    mixcr_drop_outliers = true
+    mixcr_overlap_criteria = "CDR3|AA|V|J"
+    mixcr_diversity_plottype = "boxplot"
+
+
+    // Input data
+    input = pipelines_testdata_base_path + 'testdata-sc/10x_sc_raw.tsv'
+    reference_10x = pipelines_testdata_base_path + 'testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
+    imgt_mixcr = "https://github.com/repseqio/library-imgt/releases/download/v8/imgt.202312-3.sv8.json.gz"
+}