Merge branch 'master' into umitools_nftest

.github/CODEOWNERS

@@ -12,3 +12,4 @@ modules/nf-core/pints/caller/** @edmundmiller
 modules/nf-core/preseq/ccurve/** @edmundmiller
 modules/nf-core/preseq/lcextrap/** @edmundmiller
 subworkflows/nf-core/homer/** @edmundmiller
+modules/nf-core/**/Dockerfile @edmundmiller @maxulysse

.github/actions/nf-test-action/action.yml

@@ -0,0 +1,100 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  tags:
+    description: "Tags to test (`<tags>[,<tags>...]`)"
+    required: false
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      with:
+        distribution: "temurin"
+        java-version: "17"
+
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      with:
+        python-version: "3.11"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFTEST_VERSION }}"
+        install-pdiff: true
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: ${{inputs.profile == 'conda'}}
+      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+    # Set up secrets
+    - name: Set up nextflow secrets
+      if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
+      shell: bash
+      run: |
+        python -m pip install cryptography
+        nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
+        SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
+        NFT_WORKDIR: "~"
+      run: |
+        nf-test test \
+          --profile=${{ inputs.profile }} \
+          --tap=test.tap \
+          --verbose \
+          --ci \
+          --changed-since HEAD^ \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
+          --filter process,workflow \
+          --follow-dependencies \
+          ${{ env.TAGS }}
+
+      # TODO If no test.tap, then make one to spoof?
+    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+      if: ${{ inputs.path != '' }}
+      with:
+        path: >-
+          test.tap
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/

.github/conda_skip.yml

@@ -0,0 +1,184 @@
+# TODO What do we do with these?
+# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now
+exclude:
+  - path: modules/nf-core/nf-test
+  - profile: conda
+    path: modules/nf-core/angsd/gl
+  - profile: conda
+    path: modules/nf-core/annotsv/installannotations
+  - profile: conda
+    path: modules/nf-core/happy/sompy
+  - profile: conda
+    path: modules/nf-core/backsub
+  - profile: conda
+    path: modules/nf-core/bakta/bakta
+  - profile: conda
+    path: modules/nf-core/bakta/baktadbdownload
+  - profile: conda
+    path: modules/nf-core/bases2fastq
+  - profile: conda
+    path: modules/nf-core/bcl2fastq
+  - profile: conda
+    path: modules/nf-core/bclconvert
+  - profile: conda
+    path: modules/nf-core/celesta
+  - profile: conda
+    path: modules/nf-core/cellpose
+  - profile: conda
+    path: modules/nf-core/cellranger/count
+  - profile: conda
+    path: modules/nf-core/cellranger/mkfastq
+  - profile: conda
+    path: modules/nf-core/cellranger/mkgtf
+  - profile: conda
+    path: modules/nf-core/cellranger/mkref
+  - profile: conda
+    path: modules/nf-core/cellranger/mkvdjref
+  - profile: conda
+    path: modules/nf-core/cellranger/multi
+  - profile: conda
+    path: modules/nf-core/cellranger/vdj
+  - profile: conda
+    path: modules/nf-core/checkqc
+  - profile: conda
+    path: modules/nf-core/custom/dumpsoftwareversions
+  - profile: conda
+    path: modules/nf-core/deepcell/mesmer
+  - profile: conda
+    path: modules/nf-core/deepsomatic
+  - profile: singularity
+    path: modules/nf-core/deepsomatic
+  - profile: conda
+    path: modules/nf-core/deepvariant
+  - profile: conda
+    path: modules/nf-core/deepvariant/callvariants
+  - profile: conda
+    path: modules/nf-core/deepvariant/makeexamples
+  - profile: conda
+    path: modules/nf-core/deepvariant/postprocessvariants
+  - profile: conda
+    path: modules/nf-core/deepvariant/rundeepvariant
+  - profile: conda
+    path: modules/nf-core/deepvariant/vcfstatsreport
+  - profile: conda
+    path: modules/nf-core/doubletdetection
+  - profile: conda
+    path: modules/nf-core/ensemblvep/vep
+  - profile: conda
+    path: modules/nf-core/fastk/fastk
+  - profile: conda
+    path: modules/nf-core/cellrangerarc/mkgtf
+  - profile: conda
+    path: modules/nf-core/fastk/histex
+  - profile: conda
+    path: modules/nf-core/fastk/merge
+  - profile: conda
+    path: modules/nf-core/fcs/fcsadaptor
+  - profile: conda
+    path: modules/nf-core/fcs/fcsgx
+  - profile: conda
+    path: modules/nf-core/ganon/buildcustom
+  - profile: conda
+    path: modules/nf-core/ganon/classify
+  - profile: conda
+    path: modules/nf-core/ganon/report
+  - profile: conda
+    path: modules/nf-core/ganon/table
+  - profile: conda
+    path: modules/nf-core/gatk4/cnnscorevariants
+  - profile: conda
+    path: modules/nf-core/gatk4/determinegermlinecontigploidy
+  - profile: conda
+    path: modules/nf-core/genescopefk
+  - profile: conda
+    path: modules/nf-core/ilastik/multicut
+  - profile: conda
+    path: modules/nf-core/ilastik/pixelclassification
+  - profile: conda
+    path: modules/nf-core/imputeme/vcftoprs
+  - profile: conda
+    path: modules/nf-core/mcstaging/imc2mc
+  - profile: conda
+    path: modules/nf-core/mcquant
+  - profile: conda
+    path: modules/nf-core/mcstaging/phenoimager2mc
+  - profile: conda
+    path: modules/nf-core/merquryfk/katcomp
+  - profile: conda
+    path: modules/nf-core/merquryfk/katgc
+  - profile: conda
+    path: modules/nf-core/merquryfk/merquryfk
+  - profile: conda
+    path: modules/nf-core/merquryfk/ploidyplot
+  - profile: conda
+    path: modules/nf-core/molkartgarage/clahe
+  - profile: conda
+    path: modules/nf-core/quartonotebook
+  - profile: conda
+    path: modules/nf-core/scimap/spatiallda
+  - profile: conda
+    path: modules/nf-core/sentieon/bwaindex
+  - profile: conda
+    path: modules/nf-core/sentieon/bwamem
+  - profile: conda
+    path: modules/nf-core/sentieon/datametrics
+  - profile: conda
+    path: modules/nf-core/sentieon/dedup
+  - profile: conda
+    path: modules/nf-core/sentieon/qualcal
+  - profile: conda
+    path: modules/nf-core/spaceranger/mkgtf
+  - profile: conda
+    path: modules/nf-core/spaceranger/mkref
+  - profile: conda
+    path: modules/nf-core/spaceranger/count
+  - profile: conda
+    path: modules/nf-core/spotiflow
+  - profile: conda
+    path: modules/nf-core/svanalyzer/svbenchmark
+  - profile: conda
+    path: modules/nf-core/universc
+  - profile: singularity
+    path: modules/nf-core/universc
+  - profile: conda
+    path: modules/nf-core/vt/decompose
+  - profile: singularity
+    path: modules/nf-core/bases2fastq
+  - profile: conda
+    path: modules/nf-core/wittyer
+  - profile: conda
+    path: modules/nf-core/islandpath
+  - profile: conda
+    path: modules/nf-core/scimap/mcmicro
+  - profile: conda
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: docker_self_hosted
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: singularity
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: conda
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: docker_self_hosted
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: singularity
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: conda
+    path: subworkflows/nf-core/vcf_annotate_ensemblvep
+  - profile: conda
+    path: subworkflows/nf-core/bcl_demultiplex
+  - profile: conda
+    path: subworkflows/nf-core/deepvariant
+  - profile: conda
+    path: subworkflows/nf-core/fastq_align_bamcmp_bwa
+  - profile: conda
+    path: subworkflows/nf-core/fastq_align_bwa
+  - profile: conda
+    path: subworkflows/nf-core/fasta_newick_epang_gappa
+  - profile: conda
+    path: modules/nf-core/xeniumranger/relabel
+  - profile: conda
+    path: modules/nf-core/xeniumranger/rename
+  - profile: conda
+    path: modules/nf-core/xeniumranger/resegment
+  - profile: conda
+    path: modules/nf-core/xeniumranger/import-segmentation

.github/renovate.json5

@@ -1,79 +1,30 @@
 {
-    $schema: "https://docs.renovatebot.com/renovate-schema.json",
-    extends: ["config:best-practices"],
-    vulnerabilityAlerts: {
-        labels: ["security"],
-        schedule: "at any time",
-    },
-    prHourlyLimit: 3,
-    platform: "github",
-    onboarding: false,
-    dependencyDashboard: true,
-    dependencyDashboardTitle: "Renovate Dashboard 🤖",
-    suppressNotifications: ["prIgnoreNotification"],
-    rebaseWhen: "conflicted",
-    reviewers: ["team:modules"],
-    assigneesFromCodeOwners: true,
-    gitAuthor: "nf-core-bot <[email protected]>",
-    prHeader: "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
-    "pre-commit": {
-        enabled: true,
-    },
-    customManagers: [
-    // TODO waiting on https://github.com/nf-core/modules/pull/4080
-        // {
-        //     customType: "regex",
-        //     description: "Process Containers dependencies",
-        //     fileMatch: ["(^|/)main\\.nf$"],
-        //     matchStrings: [
-        //         "\\s+'(?<depName>\\S+):(?<currentValue>.*\\-.*)' }\"\n",
-        //     ],
-        //     datasourceTemplate: "docker",
-        // },
-        // {
-        //     customType: "regex",
-        //     description: "Upgrade conda dependencies",
-        //     fileMatch: ["(^|/)environment(.*).ya?ml$"],
-        //     matchStrings: [
-        //         '#\\s*renovate\\s+datasource=conda\\s+depName=(?<depName>.*?)\\s+-\\s*[\\w-]+\\s*==?\\s*"?(?<currentValue>.*)"?',
-        //         '# renovate: datasource=conda depName=(?<depName>.*?)\\s+-\\s*[\\w-]+\\s*==?\\s*"?(?<currentValue>.*)"?',
-        //     ],
-        //     datasourceTemplate: "conda",
-        // },
-        // {
-        //     customType: "regex",
-        //     description: "Upgrade pypi dependencies inside conda environment files",
-        //     fileMatch: ["(^|/)environment(.*).ya?ml$"],
-        //     matchStrings: [
-        //         "# renovate datasource=pypi\\s+-\\s*(?<depName>[\\w-]+)\\s*(\\[[\\w,\\s]+\\])?\\s*==?\\s*(?<currentValue>.*)",
-        //         "# renovate: datasource=pypi\\s+-\\s*(?<depName>[\\w-]+)\\s*(\\[[\\w,\\s]+\\])?\\s*==?\\s*(?<currentValue>.*)",
-        //     ],
-        //     datasourceTemplate: "pypi",
-        // },
-        ],
-    packageRules: [
-        {
-            matchDatasources: ["docker"],
-            registryUrls: ["quay.io"],
-        },
-        {
-            matchManagers: ["github-actions"],
-            automerge: true,
-            pinDigest: {
-                enabled: false,
-            },
-            matchPackageNames: ["/^nf-core//", "/^seqera/"],
-        },
-        {
-            matchManagers: ["github-actions"],
-            groupName: "GitHub Actions",
-            automerge: true,
-            schedule: ["before 9am"],
-        },
+    "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+    "extends": [
+        "github>nf-core/ops//.github/renovate/default.json5",
+        "github>nf-core/ops//.github/renovate/process_updaters.json5"
+    ],
+    "prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
+    "packageRules": [
         {
-            automerge: true,
-            schedule: ["before 9am on Monday"],
-            matchPackageNames: ["/renovate-config-validator/"],
-        },
+            "matchDatasources": [
+                "conda",
+                "pypi",
+                "docker"
+            ],
+            "automerge": false
+        }
     ],
+        "customManagers": [
+            {
+                "customType": "regex",
+                "fileMatch": [
+                    "(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$",
+                    "(^|/)action\\.ya?ml$"
+                ],
+                "matchStrings": [
+                    "# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
+                ]
+            }
+        ]
 }