Adds system testing workflow to github actions

.github/pull_request_template.md

@@ -8,7 +8,6 @@ Please fill in the checklist below and comment as needed.
 - [ ] Is this a feature addition? Briefly describe.
 - [ ] Did you modify QuaC-Watch config file? If so, did you modify multiqc template
   `configs/multiqc_config_template.jinja2` and script `src/quac_watch/create_mutliqc_configs.py` as necessary?
-- [ ] Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why?
 - [ ] Updated `Changelog.md` file with change logs in recommended format?
 
 

.github/workflows/system_testing.yml

@@ -0,0 +1,127 @@
+name: system_testing
+# on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    paths:
+      - '.github/workflows/system_testing.yml'
+      - '.test/**'
+      - 'configs/**'
+      - 'src/**'
+      - 'workflow/**'
+  pull_request:
+    paths:
+      - '.github/workflows/system_testing.yml'
+      - '.test/**'
+      - 'configs/**'
+      - 'src/**'
+      - 'workflow/**'
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+      - converted_to_draft
+  workflow_dispatch:
+
+jobs:
+  system-testing:
+    name: System testing - QuaC
+    runs-on: ubuntu-20.04
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: checkout repository
+        uses: actions/checkout@v2
+
+      - name: Create quac environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          activate-environment: quac
+          environment-file: configs/env/quac.yaml
+
+      - name: Check conda solution
+        run: |
+          mamba env export
+
+      - name: Check snakemake exists in conda env
+        run: |
+          which snakemake
+          snakemake --version
+
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+      - name: Check singularity is working
+        run: |
+          singularity  --version
+
+      - name: Set up dependencies for QuaC
+        run: |
+          bash src/setup_dependency_datasets.sh
+
+      - name: Run QuaC system testing - WGS mode AND no prior QC data
+        run: |
+          PROJECT_CONFIG="project_2samples"
+          PRIOR_QC_STATUS="no_priorQC"
+          USE_SLURM=""
+          python src/run_quac.py \
+                --project_name test_project \
+                --projects_path ".test/ngs-data/" \
+                --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \
+                --outdir "data/quac/results/test_${PROJECT_CONFIG}_wgs-${PRIOR_QC_STATUS}/analysis" \
+                --quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \
+                --workflow_config "configs/workflow.yaml" \
+                $USE_SLURM
+
+      - name: Run QuaC system testing - Exome mode AND no prior QC data
+        run: |
+          PROJECT_CONFIG="project_2samples"
+          PRIOR_QC_STATUS="no_priorQC"
+          USE_SLURM=""
+          python src/run_quac.py \
+                --project_name test_project \
+                --projects_path ".test/ngs-data/" \
+                --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \
+                --outdir "data/quac/results/test_${PROJECT_CONFIG}_exome-${PRIOR_QC_STATUS}/analysis" \
+                --quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
+                --workflow_config "configs/workflow.yaml" \
+                --exome \
+                $USE_SLURM
+
+      - name: Run QuaC system testing - WGS mode AND uses prior QC data
+        run: |
+          PROJECT_CONFIG="project_2samples"
+          PRIOR_QC_STATUS="include_priorQC"
+          USE_SLURM=""
+          python src/run_quac.py \
+                --project_name test_project \
+                --projects_path ".test/ngs-data/" \
+                --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \
+                --outdir "data/quac/results/test_${PROJECT_CONFIG}_wgs-${PRIOR_QC_STATUS}/analysis" \
+                --quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \
+                --include_prior_qc \
+                --allow_sample_renaming \
+                --workflow_config "configs/workflow.yaml" \
+                $USE_SLURM
+
+      - name: Run QuaC system testing - Exome mode AND uses prior QC data
+        run: |
+          PROJECT_CONFIG="project_2samples"
+          PRIOR_QC_STATUS="include_priorQC"
+          USE_SLURM=""
+          python src/run_quac.py \
+                --project_name test_project \
+                --projects_path ".test/ngs-data/" \
+                --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \
+                --outdir "data/quac/results/test_${PROJECT_CONFIG}_exome-${PRIOR_QC_STATUS}/analysis" \
+                --quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
+                --exome \
+                --include_prior_qc \
+                --allow_sample_renaming \
+                --workflow_config "configs/workflow.yaml" \
+                $USE_SLURM

docs/Changelog.md

@@ -12,6 +12,10 @@ YYYY-MM-DD  John Doe
 ```
 ---
 
+2023-05-31  Manavalan Gajapathy
+
+* Adds system testing as github actions workflow
+
 2023-05-09  Manavalan Gajapathy
 
 * Adds a verification step in the CLI wrapper script to check if the file/dirpaths to be mounted to singularity already exist as expected (#71)