Merge pull request genomic-medicine-sweden#70 from genomic-medicine-s…

…weden/output_structure

feat: adapt results output structure to better match current GMS560 p…

.github/workflows/integration1.yaml

@@ -16,11 +16,6 @@ jobs:
     name: integration small data set singularity
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -34,6 +29,11 @@ jobs:
       - name: Set strict channels
         run: |
           conda config --set channel_priority strict
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/lint.yaml

@@ -25,9 +25,6 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/pycodestyl.yaml

@@ -25,16 +25,6 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-            activate-environment: my-env
-            use-mamba: true
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

config/output_files.yaml

@@ -1,21 +1,21 @@
 files:
   - name: "_copy_detected_variants"
     input: "pgx/detected_variants/{sample}_{type}.annotated.csv"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.detected_variants.csv"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.detected_variants.csv"
     types:
       - T
       - N
 
   - name: "_copy_depth_of_baits"
     input: "pgx/depth_of_coverage/depth_of_baits/{sample}_{type}.output.gdf"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.depth_of_baits.gdf"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.depth_of_baits.gdf"
     types:
       - T
       - N
 
   - name: "_copy_depth_at_missing"
     input: "pgx/append_id_to_gdf/{sample}_{type}.depth_at_missing_annotated.gdf"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.depth_at_missing_annotated.gdf"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.depth_at_missing_annotated.gdf"
     types:
       - T
       - N
@@ -39,4 +39,4 @@ files:
     output: "results/dna/pgx/{sample}_{type}.pgx_report.html"
     types:
       - T
-      - N
+      - N

requirements.txt

@@ -1,8 +1,9 @@
 hydra-genetics==0.15.0
 pandas>=1.3.1
-snakemake==7.8.0
+snakemake==7.18.0
 singularity==3.0.0
 jinja2==3.0.1
 networkx
 tabulate<0.9.0
-pulp < 2.8
+pulp<2.8
+smart_open<7.0.0