From b399c7601ebc2ec3bc678c78a5c254aa10471536 Mon Sep 17 00:00:00 2001 From: Kayla Meyer Date: Thu, 23 May 2024 16:14:26 +0200 Subject: [PATCH] update github actions config file path --- .github/workflows/github-actions.yml | 18 ++++--- .../test_data/training/deeprvat_config.yaml | 52 +++++++------------ 2 files changed, 30 insertions(+), 40 deletions(-) diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml index 3708d48b..ff4784da 100644 --- a/.github/workflows/github-actions.yml +++ b/.github/workflows/github-actions.yml @@ -53,12 +53,13 @@ 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 @@ -66,7 +67,8 @@ jobs: - 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 . @@ -99,7 +101,7 @@ 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} @@ -107,7 +109,7 @@ jobs: 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 index 233baf7e..63a6a7a3 100644 --- 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