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Merge branch 'master' into update-panaroo/run
* master: (120 commits) Use long form docker.io address for Ubuntu (nf-core#3358) Default registry to quay.io (nf-core#3344) Sbwf impute glimpse2 (nf-core#3349) added cellranger vdj/mkvdjref modules, with module test for vdj (nf-core#3033) Add space to fix singularity download error on shinyngs modules (nf-core#3351) Output channel modification star (nf-core#3350) fix corrected typo in output (nf-core#3337) give execution permissions to dumpsoftwareversions.py (nf-core#3347) fix meta.ymls for dumpsoftware and multiqc (nf-core#3345) Fixing failing subworkflow tests (nf-core#3343) remove imputeme module since it is evidently no longer supported (nf-core#3223) Update path for yaml-schema json (nf-core#3340) New module MetaPhlAn4 (nf-core#3298) Update ALL bcftools modules (nf-core#3339) update docker and singularity version of p7zip (nf-core#3338) update sratools/fasterqdump to handle 10X data (nf-core#3336) Make MAD plots optional in shinyngs (nf-core#3334) reset tools in CI to released version (nf-core#3335) new module wisecondorx/gender (nf-core#3333) Bump shinyngs modules (nf-core#3323) ...
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,182 @@ | ||
| name: nf-test | ||
| on: | ||
| push: | ||
| branches: [master] | ||
| pull_request: | ||
| branches: [master] | ||
| merge_group: | ||
| types: [checks_requested] | ||
| branches: [master] | ||
|
|
||
| # Cancel if a newer run is started | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| changes: | ||
| name: Check for changes | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| # Expose matched filters as job 'modules' output variable | ||
| modules: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: dorny/paths-filter@v2 | ||
| id: filter | ||
| with: | ||
| filters: "tests/config/nftest_modules.yml" | ||
|
|
||
| test: | ||
| runs-on: ubuntu-20.04 | ||
|
|
||
| name: ${{ matrix.tags }} ${{ matrix.profile }} | ||
| needs: changes | ||
| if: needs.changes.outputs.modules != '[]' | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| tags: ["${{ fromJson(needs.changes.outputs.modules) }}"] | ||
| profile: ["docker", "singularity", "conda"] | ||
| exclude: | ||
| - profile: "conda" | ||
| tags: annotsv | ||
| - profile: "conda" | ||
| tags: bases2fastq | ||
| - profile: "conda" | ||
| tags: bcl2fastq | ||
| - profile: "conda" | ||
| tags: bclconvert | ||
| - profile: "conda" | ||
| tags: cellranger/count | ||
| - profile: "conda" | ||
| tags: cellranger/mkfastq | ||
| - profile: "conda" | ||
| tags: cellranger/mkgtf | ||
| - profile: "conda" | ||
| tags: cellranger/mkref | ||
| - profile: "conda" | ||
| tags: deepvariant | ||
| - profile: "conda" | ||
| tags: ensemblvep/vep | ||
| - profile: "conda" | ||
| tags: fastk/fastk | ||
| - profile: "conda" | ||
| tags: fastk/histex | ||
| - profile: "conda" | ||
| tags: fastk/merge | ||
| - profile: "conda" | ||
| tags: fcs/fcsadaptor | ||
| - profile: "conda" | ||
| tags: fcs/fcsgx | ||
| - profile: "conda" | ||
| tags: gatk4/cnnscorevariants | ||
| - profile: "conda" | ||
| tags: gatk4/determinegermlinecontigploidy | ||
| - profile: "conda" | ||
| tags: genescopefk | ||
| - profile: "conda" | ||
| tags: ilastik/multicut | ||
| - profile: "conda" | ||
| tags: ilastik/pixelclassification | ||
| - profile: "conda" | ||
| tags: imputeme/vcftoprs | ||
| - profile: "conda" | ||
| tags: merquryfk/katcomp | ||
| - profile: "conda" | ||
| tags: merquryfk/katgc | ||
| - profile: "conda" | ||
| tags: merquryfk/merquryfk | ||
| - profile: "conda" | ||
| tags: merquryfk/ploidyplot | ||
| - profile: "conda" | ||
| tags: sentieon/bwaindex | ||
| - profile: "conda" | ||
| tags: sentieon/bwamem | ||
| - profile: "conda" | ||
| tags: universc | ||
| - profile: "singularity" | ||
| tags: universc | ||
| - profile: "conda" | ||
| tags: subworkflows/vcf_annotate_ensemblvep | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: actions/cache@v3 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install Nextflow | ||
| env: | ||
| CAPSULE_LOG: none | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Cache nf-test installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: ${{ runner.os }}-nftest | ||
|
|
||
| - name: Install nf-test | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
|
|
||
| - name: Set up miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| - name: Conda setup | ||
| if: matrix.profile == 'conda' | ||
| run: | | ||
| conda clean -a | ||
| conda install -n base conda-libmamba-solver | ||
| conda config --set solver libmamba | ||
| # Set up secrets | ||
| - name: Set up nextflow secrets | ||
| if: env.SENTIEON_LICENSE_BASE64 != null | ||
| run: | | ||
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | ||
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | ||
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | ||
| SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | ||
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | ||
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | ||
| # Test the module | ||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test \ | ||
| --profile=${{ matrix.profile }} \ | ||
| --tag ${{ matrix.tags }} \ | ||
| --tap=test.tap | ||
| - uses: pcolby/tap-summary@v1 | ||
| with: | ||
| path: >- | ||
| test.tap |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,6 +2,7 @@ | |
| work/ | ||
| results/ | ||
| test_output/ | ||
| .nf-test/ | ||
| output/ | ||
| .DS_Store | ||
| *.code-workspace | ||
|
|
||
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