Snakedeploy Tests

- runs V-pipe straight from the git as per Snakemake Workflow Catalog

.github/workflows/snakedeploy_tests.yaml

@@ -0,0 +1,144 @@
+name: Snakedeploy
+
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  runtime_tests:
+    env:
+        THREADS: 5
+
+    strategy:
+      max-parallel: 5
+      fail-fast: false
+      matrix:
+         # python-version: [ "3.11"]
+         virus: ["hiv"]
+         #, "sars-cov-2"]
+
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout test data
+        uses: actions/checkout@v3
+        with:
+            sparse-checkout: |
+                tests
+            sparse-checkout-cone-mode: false
+            lfs: false
+            # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
+
+      - name: Install conda environment dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          # python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,bioconda
+          channel-priority: strict
+          activate-environment: snakemake
+          auto-update-conda: true
+          environment-file: tests/conda_test_env.yaml
+
+      - name: Snakedeploy
+        # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out
+        run: |
+            snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)"
+
+      - name: Configure
+        run: |
+            virus="${{ matrix.virus }}"
+            threads="${THREADS}"
+            trim_primers="false"
+
+            # samples data
+            data_root="tests/data/${virus}"
+            mkdir -p samples
+            mv -v "${data_root}"/*/ samples/
+
+            if [ -e "${data_root}/samples.tsv" ]; then
+                mv -v "${data_root}/samples.tsv" samples/
+                # automatically turn trimming on if 4-columns format in TSV
+                # shellcheck disable=SC2162
+                while read s b l p o; do
+                    # no proto?
+                    if [[ -z "${p}" ]]; then
+                        continue
+                    fi
+
+                    # proto => trim!
+                    trim_primers="true"
+                    echo "with trimming"
+                    break
+
+                    : "${s} ${b} ${l} ${o}" are unused
+                done < "samples/samples.tsv"
+            fi
+
+            # configuration file
+            cat > config/config.yaml <<CONFIG
+            general:
+                virus_base_config: "${virus}"
+
+            output:
+                snv: true
+                local: true
+                global: false
+                visualization: true
+                diversity: true
+                QA: true
+                upload: true
+                trim_primers: ${trim_primers}
+
+            upload:
+                orig_cram: true
+
+            snv:
+                threads: ${threads}
+            CONFIG
+
+            # does this test data provides extra configuration options
+            if [ -e "${data_root}/config-extra.yaml" ]; then
+                echo "with extra config:"
+                cat "${data_root}/config-extra.yaml"
+                echo
+                # recursively merge using go-yq
+                yq eval-all --inplace '. as $item ireduce ({}; . * $item )' config/config.yaml "${data_root}/config-extra.yaml"
+            fi
+
+      - name: Run test
+        run:
+            PYTHONUNBUFFERED=1 snakemake \
+                --use-conda \
+                --cores ${THREADS} \
+                --dry-run
+
+            echo
+            cat config/samples.tsv
+            echo
+
+            PYTHONUNBUFFERED=1 snakemake \
+                --use-conda \
+                --cores ${THREADS} \
+                -p \
+                --keep-going
+
+      - name: Archive test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: test_output
+          path: |
+            ./*
+            !./.git
+            !./.snakemake/conda/*/
+          if-no-files-found: ignore

README.md

@@ -81,7 +81,7 @@ docker run --rm -it -v $PWD:/work ghcr.io/cbg-ethz/v-pipe:master --jobs 4 --prin
 First install [mamba](https://github.com/conda-forge/miniforge#mambaforge), then create and activate an environment with Snakemake and Snakedeploy:
 
 ```bash
-mamba create -c bioconda -c conda-forge --name snakemake snakemake snakedeploy
+mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
 conda activate snakemake
 ```
 

tests/conda_snakedeploy_env.yaml

@@ -0,0 +1,8 @@
+name: snakemake
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - snakemake-minimal
+  - snakedeploy
+  - go-yq