Merge pull request #119 from hydra-genetics/develop

chore: dev to master

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

@@ -0,0 +1,34 @@
+
+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

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

.tests/integration/config.yaml

@@ -36,6 +36,8 @@ multiqc:
       included_unit_types: ['N', 'T']
       qc_files:
         - "qc/fastqc/{sample}_{type}_{flowcell}_{lane}_{barcode}_{read}_fastqc.zip"
+        - "qc/peddy/peddy.sex_check.csv"
+        - "qc/peddy/peddy.ped_check.csv"
         - "qc/picard_collect_alignment_summary_metrics/{sample}_{type}.alignment_summary_metrics.txt"
         - "qc/picard_collect_duplication_metrics/{sample}_{type}.duplication_metrics.txt"
         - "qc/picard_collect_gc_bias_metrics/{sample}_{type}.gc_bias.summary_metrics"
@@ -89,3 +91,9 @@ rseqc_gene_body_coverage:
 rseqc_inner_distance:
   bed: "reference/gene_model.bed"
   container: "docker://hydragenetics/rseqc:4.0.0"
+
+verifybamid2:
+  container: "docker://hydragenetics/verifybamid2:2.0.1"
+  svd_mu: "verifybamid2/1000g.phase3.10k.b38.exome.vcf.gz.dat.mu"
+
+