From 2a444c60d5d70ae779e5a5ce8de2d6da6838c96b Mon Sep 17 00:00:00 2001
From: Magnus Wahlberg <endast@gmail.com>
Date: Thu, 19 Oct 2023 11:02:48 +0200
Subject: [PATCH] Restore all pipelines

---
 .github/workflows/github-actions.yml | 123 +++++++++++++++++++++++++++
 1 file changed, 123 insertions(+)

diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml
index 61eb3a17..1fecb38c 100644
--- a/.github/workflows/github-actions.yml
+++ b/.github/workflows/github-actions.yml
@@ -4,6 +4,88 @@ on: [ push ]
 
 jobs:
 
+  DeepRVAT-Pipeline-Smoke-Tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Training Association Testing smoke test
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: 'example'
+          snakefile: 'pipelines/training_association_testing.snakefile'
+          args: '-j 2 -n'
+      - name: Link pretrained models
+        run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
+      - name: Association Testing Pretrained Smoke Test
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: 'example'
+          snakefile: 'pipelines/association_testing_pretrained.snakefile'
+          args: '-j 2 -n'
+      - name: Seed Gene Discovery Smoke Test
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: 'example'
+          snakefile: 'pipelines/seed_gene_discovery.snakefile'
+          args: '-j 2 -n'
+
+  DeepRVAT-Pipeline-Tests:
+    runs-on: ubuntu-latest
+    needs: DeepRVAT-Pipeline-Smoke-Tests
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1.4.3
+        with:
+          environment-name: deeprvat-gh-action
+          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
+          cache-environment: true
+          cache-downloads: true
+      - name: Install DeepRVAT
+        run: pip install -e ${{ github.workspace }}
+        shell: micromamba-shell {0}
+      # There are no GPUs on the gh worker, so we disable it in the config
+      - name: Update config to use no gpus
+        run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/example/config.yaml"
+        shell: bash -el {0}
+      - name: Run training_association_testing pipeline
+        run: |
+          python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
+          --snakefile ${{ github.workspace }}/pipelines/training_association_testing.snakefile --show-failed-logs
+        shell: micromamba-shell {0}
+      - name: Link pretrained models
+        run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
+        shell: bash -el {0}
+      - name: Run association_testing_pretrained pipeline
+        run: |
+          python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
+          --snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained.snakefile --show-failed-logs
+        shell: micromamba-shell {0}
+      - name: Copy seed gene discovery snakemake config
+        run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml .
+        shell: bash -el {0}
+      - name: Run seed_gene_discovery pipeline
+        run: |
+          python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
+          --snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs
+        shell: micromamba-shell {0}
+
+
+  DeepRVAT-Preprocessing-Pipeline-Smoke-Tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Preprocessing Smoke Test
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: 'example/preprocess'
+          snakefile: 'pipelines/preprocess.snakefile'
+          args: '-j 2 -n --configfile pipelines/config/deeprvat_preprocess_config.yaml'
+          stagein: 'touch example/preprocess/workdir/reference/GRCh38.primary_assembly.genome.fa'
+
+
   DeepRVAT-Annotation-Pipeline-Smoke-Tests:
     runs-on: ubuntu-latest
     steps:
@@ -15,3 +97,44 @@ jobs:
           directory: 'example/annotations'
           snakefile: 'pipelines/annotations.snakefile'
           args: '-j 2 -n --configfile pipelines/config/deeprvat_annotation_config.yaml'
+
+
+  DeepRVAT-Preprocessing-Pipeline-Tests:
+    runs-on: ubuntu-latest
+    needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests
+    steps:
+
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1.4.3
+        with:
+          environment-name: deeprvat-preprocess-gh-action
+          environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install DeepRVAT
+        run: pip install -e ${{ github.workspace }}
+        shell: micromamba-shell {0}
+
+      - name: Cache Fasta file
+        id: cache-fasta
+        uses: actions/cache@v3
+        with:
+          path: example/preprocess/workdir/reference
+          key: ${{ runner.os }}-reference-fasta
+
+      - name: Download and unpack fasta data
+        if: steps.cache-fasta.outputs.cache-hit != 'true'
+        run: |
+          cd ${{ github.workspace }}/example/preprocess && \
+          wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \
+          -O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \
+          && gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz
+
+      - name: Run preprocessing pipeline
+        run: |
+          python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
+          --snakefile ${{ github.workspace }}/pipelines/preprocess.snakefile \
+          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+        shell: micromamba-shell {0}