Merge pull request #81 from hydra-genetics/develop

chore: dev to master

.github/workflows/integration.yaml

@@ -16,22 +16,22 @@ jobs:
     name: integration small data set singularity
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
-      - name: Setup Mambaforge
+      - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v2
         with:
-            miniforge-variant: Mambaforge
+            miniforge-variant: Miniforge3
             miniforge-version: latest
             activate-environment: my-env
             use-mamba: true
       - name: Set strict channel and install singularity
         run: |
           conda config --set channel_priority strict
-          mamba install -c conda-forge -c bioconda singularity=3.8.6
+          mamba install -c conda-forge -c bioconda apptainer=1.3.2
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/test-build-mkdocs.yaml

@@ -0,0 +1,33 @@
+name: build mkdocs
+
+on:
+  push:
+    branches:
+     - develop
+     - master
+  pull_request:
+    branches:
+     - develop
+     - master
+  workflow_dispatch:
+
+jobs:
+  build-mkdocs:
+    name: build mkdocs
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+          pip install -r docs/requirements.txt
+      - name: build mkdocs
+        run: |
+          mkdocs build

docs/requirements.txt

@@ -6,5 +6,5 @@ mkdocs-schema-reader==0.11.1
 mkdocs-simple-hooks==0.1.5
 mdx_spanner==0.0.5
 mkdocs-yaml-schema-plugin==0.2.3
-mkdocs-snakemake-rule-plugin==0.3.1
+mkdocs-snakemake-rule-plugin==0.3.3
 mkdocs-material==9.1.7

requirements.txt

@@ -1,7 +1,8 @@
-drmaa==0.7.9
-hydra-genetics==0.15.0
+hydra-genetics==3.0.0
 jinja2==3.0.1
+networkx==2.5
 pandas>=1.3.1
-snakemake>=7.18.0,<8
+pulp<2.8
 singularity==3.0.0
+snakemake>=7.18.0,<8
 tabulate<0.9.0

workflow/rules/optitype.smk

@@ -14,9 +14,9 @@ rule optitype:
         out_dir=temp(directory("biomarker/optitype/{sample}_{type}/")),
     params:
         extra=config.get("optitype", {}).get("extra", ""),
-        out_prefix="{sample}_{type}_hla_type",
         sample_type=config.get("optitype", {}).get("sample_type", "-d"),
         enumeration=config.get("optitype", {}).get("enumeration", "4"),
+        prefix=config.get("optitype", {}).get("prefix", "{sample}_{type}"),
     log:
         "biomarker/optitype/{sample}_{type}/{sample}_{type}_hla_type_result.tsv.log",
     benchmark:
@@ -40,5 +40,6 @@ rule optitype:
         "-i {input.fastq1} {input.fastq2} "
         "{params.sample_type} "
         "--enumerate {params.enumeration} "
-        "-p {params.out_prefix} "
-        "-o {output.out_dir}) &> {log}"
+        "-o {output.out_dir} && "
+        "mv {output.out_dir}/*/*.pdf {output.out_dir}/{params.prefix}_hla_type_coverage_plot.pdf && "
+        "mv {output.out_dir}/*/*.tsv {output.out_dir}/{params.prefix}_hla_type_result.tsv) &> {log}"