From 1702cdbd19d226f4568927b6bd3900d9720da243 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Wed, 26 Jul 2023 22:43:15 +0200
Subject: [PATCH] Snakedeploy Tests

- runs V-pipe straight from the git as per Snakemake Workflow Catalog
---
 .github/workflows/snakedeploy_tests.yaml | 87 ++++++++++++++++++++++++
 README.md                                |  2 +-
 tests/conda_snakedeploy_env.yaml         |  8 +++
 tests/configure_for_virus.sh             | 81 ++++++++++++++++++++++
 4 files changed, 177 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/snakedeploy_tests.yaml
 create mode 100644 tests/conda_snakedeploy_env.yaml
 create mode 100755 tests/configure_for_virus.sh

diff --git a/.github/workflows/snakedeploy_tests.yaml b/.github/workflows/snakedeploy_tests.yaml
new file mode 100644
index 00000000..c0cb35b7
--- /dev/null
+++ b/.github/workflows/snakedeploy_tests.yaml
@@ -0,0 +1,87 @@
+name: Snakedeploy
+
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  runtime_tests:
+    env:
+        THREADS: 5
+
+    strategy:
+      max-parallel: 5
+      fail-fast: false
+      matrix:
+         # python-version: [ "3.11"]
+         virus: ["hiv"]
+         #, "sars-cov-2"]
+
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout test data
+        uses: actions/checkout@v3
+        with:
+            sparse-checkout: |
+                tests
+            sparse-checkout-cone-mode: false
+            lfs: false
+            # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
+
+      - name: Install conda environment dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          # python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,bioconda
+          channel-priority: strict
+          activate-environment: snakemake
+          auto-update-conda: true
+          environment-file: tests/conda_snakedeploy_env.yaml
+
+      - name: Snakedeploy
+        # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out
+        run: |
+            snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)"
+
+      - name: Configure
+        run: |
+            tests/configure_for_virus.sh "${{ matrix.virus }}" "${THREADS}"
+
+      - name: Run test
+        run: |
+            PYTHONUNBUFFERED=1 snakemake \
+                --use-conda \
+                --cores "${THREADS}" \
+                --dry-run
+
+            echo
+            cat config/samples.tsv
+            echo
+
+            PYTHONUNBUFFERED=1 snakemake \
+                --use-conda \
+                --cores "${THREADS}" \
+                -p \
+                --keep-going
+
+      - name: Archive test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: test_output
+          path: |
+            ./*
+            !./.git
+            !./.snakemake/conda/*/
+          if-no-files-found: ignore
diff --git a/README.md b/README.md
index c449dd74..0571757d 100644
--- a/README.md
+++ b/README.md
@@ -81,7 +81,7 @@ docker run --rm -it -v $PWD:/work ghcr.io/cbg-ethz/v-pipe:master --jobs 4 --prin
 First install [mamba](https://github.com/conda-forge/miniforge#mambaforge), then create and activate an environment with Snakemake and Snakedeploy:
 
 ```bash
-mamba create -c bioconda -c conda-forge --name snakemake snakemake snakedeploy
+mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
 conda activate snakemake
 ```
 
diff --git a/tests/conda_snakedeploy_env.yaml b/tests/conda_snakedeploy_env.yaml
new file mode 100644
index 00000000..ee97b897
--- /dev/null
+++ b/tests/conda_snakedeploy_env.yaml
@@ -0,0 +1,8 @@
+name: snakemake
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - snakemake-minimal
+  - snakedeploy
+  - go-yq
diff --git a/tests/configure_for_virus.sh b/tests/configure_for_virus.sh
new file mode 100755
index 00000000..dc493130
--- /dev/null
+++ b/tests/configure_for_virus.sh
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+
+if [[ -z "$1" || "$1" == '-h' || "$1" == '--help' ]]; then
+	echo "usage:	$0 <virus> [threads]
+
+Description:
+	creates configuraiton and samples directory for virus in current working directory
+
+Arguments:
+	virus	- name of the virus to test [ 'hiv', 'sars-cov-2' ]
+	threads	- overides envrionment variable THREADS [ default: 4 ]"
+	exit 0
+fi
+
+virus="$1"
+threads="${2:-${THREADS:-4}}"
+trim_primers="false"
+
+echo "Configuring for ${virus}, using ${threads} threads"
+
+# samples data
+data_root="tests/data/${virus}"
+mkdir -p samples
+cp --link -vrf "${data_root}"/*/ samples/
+
+if [ -e "${data_root}/samples.tsv" ]; then
+	cp -vrf "${data_root}/samples.tsv" samples/
+	# automatically turn trimming on if 4-columns format in TSV
+	# shellcheck disable=SC2162
+	while read s b l p o; do
+		# no proto?
+		if [[ -z "${p}" ]]; then
+			continue
+		fi
+
+		# proto => trim!
+		trim_primers="true"
+		echo "with trimming"
+		break
+
+		: "${s} ${b} ${l} ${o}" are unused
+	done < "samples/samples.tsv"
+fi
+
+# configuration file
+cat > config/config.yaml <<CONFIG
+general:
+	virus_base_config: "${virus}"
+
+output:
+	snv: true
+	local: true
+	global: false
+	visualization: true
+	diversity: true
+	QA: true
+	upload: true
+	trim_primers: ${trim_primers}
+
+upload:
+	orig_cram: true
+
+snv:
+	threads: ${threads}
+CONFIG
+
+# does this test data provides extra configuration options
+if [ -e "${data_root}/config-extra.yaml" ]; then
+	echo "with extra config:"
+	cat "${data_root}/config-extra.yaml"
+	echo
+	# recursively merge using go-yq
+	# shellcheck disable=SC2016
+	yq eval-all --inplace '. as $item ireduce ({}; . * $item )' config/config.yaml "${data_root}/config-extra.yaml"
+fi
+
+# Display config
+echo
+echo "Configuration:"
+echo            
+yq config/config.yaml