update github actions config file path

PMBio · May 23, 2024 · b399c76 · b399c76
1 parent 6195812
commit b399c76
Show file tree

Hide file tree

Showing 2 changed files with 30 additions and 40 deletions.
diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml
@@ -53,20 +53,22 @@ jobs:
         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"
+        run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/tests/deeprvat/test_data/training/deeprvat_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
+          --snakefile ${{ github.workspace }}/pipelines/training_association_testing.snakefile --show-failed-logs \
+          --config ${{ github.workspace }}/tests/deeprvat/test_data/training/deeprvat_config.yaml
         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
+          --snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained.snakefile --show-failed-logs \
+          --config ${{ github.workspace }}/tests/deeprvat/test_data/training/deeprvat_config.yaml
         shell: micromamba-shell {0}
       - name: Copy seed gene discovery snakemake config
         run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml .
@@ -99,15 +101,15 @@ jobs:
         run: |
           python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/preprocess \
           --snakefile ${{ github.workspace }}/pipelines/preprocess_no_qc.snakefile \
-          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+          --configfile ${{ github.workspace }}/example/config/deeprvat_preprocess_config.yaml --show-failed-logs
         shell: micromamba-shell {0}
 
 
       - name: Preprocessing pipeline with qc Smoke Test
         run: |
           python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/preprocess \
           --snakefile ${{ github.workspace }}/pipelines/preprocess_with_qc.snakefile \
-          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+          --configfile ${{ github.workspace }}/example/config/deeprvat_preprocess_config.yaml --show-failed-logs
         shell: micromamba-shell {0}
 
 
@@ -126,7 +128,7 @@ jobs:
         run: |
           python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/annotations \
           --snakefile ${{ github.workspace }}/pipelines/annotations.snakefile \
-          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_annotation_config.yaml --show-failed-logs
+          --configfile ${{ github.workspace }}/example/config/deeprvat_annotation_config.yaml --show-failed-logs
         shell: micromamba-shell {0}
 
 
@@ -166,7 +168,7 @@ jobs:
         run: |
           python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
           --snakefile ${{ github.workspace }}/pipelines/preprocess_no_qc.snakefile \
-          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+          --configfile ${{ github.workspace }}/example/config/deeprvat_preprocess_config.yaml --show-failed-logs
         shell: micromamba-shell {0}
 
 
@@ -207,5 +209,5 @@ jobs:
         run: |
           python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \
           --snakefile ${{ github.workspace }}/pipelines/preprocess_with_qc.snakefile \
-          --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs
+          --configfile ${{ github.workspace }}/example/config/deeprvat_preprocess_config.yaml --show-failed-logs
         shell: micromamba-shell {0}
diff --git a/tests/deeprvat/test_data/training/deeprvat_config.yaml b/tests/deeprvat/test_data/training/deeprvat_config.yaml
@@ -1,40 +1,28 @@
 phenotypes:
-    Cholesterol:
-        correction_method: FDR
-        n_training_genes: 40
-        baseline_phenotype: Cholesterol
-    HDL_cholesterol:
-        correction_method: FDR
-        n_training_genes: 40
-        baseline_phenotype: HDL_cholesterol
-    Mean_platelet_thrombocyte_volume:
-        correction_method: FDR
-        n_training_genes: 40
-        baseline_phenotype: Mean_platelet_thrombocyte_volume
-    Platelet_crit:
-        correction_method: FDR
-        n_training_genes: 40
-        baseline_phenotype: Platelet_crit
-    Platelet_distribution_width:
-        correction_method: FDR
-        n_training_genes: 40
-        baseline_phenotype: Platelet_distribution_width
+    Cholesterol:  {}
+    HDL_cholesterol: {}
+    Mean_platelet_thrombocyte_volume: {}
+    Platelet_crit: {}
+    Platelet_distribution_width: {}
 
 baseline_results:
-    -
-        base: baseline_results
-        type: plof/burden
-    -
-        base: baseline_results
-        type: missense/burden
-    -
-        base: baseline_results
-        type: plof/skat
-    -
-        base: baseline_results
-        type: missense/skat
+    correction_method: Bonferroni
+    options:
+        -
+            base: baseline_results
+            type: plof/burden
+        -
+            base: baseline_results
+            type: missense/burden
+        -
+            base: baseline_results
+            type: plof/skat
+        -
+            base: baseline_results
+            type: missense/skat
 
 alpha: 0.05
+cv_exp: False
 
 n_burden_chunks: 4
 n_regression_chunks: 2