feat: addition of snakemake compatible format and linting (#104)

.github/workflows/ci.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
 
-  snakemake-graphs:
+  snakemake-graphs-format:
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -36,20 +36,30 @@ jobs:
       - name: Update zarp env with root. packages
         run: mamba env update -n zarp -f install/environment.root.yml
 
+      - name: Update zarp env with dev. packages
+        run: mamba env update -n zarp -f install/environment.dev.yml
+
       - name: Display all miniconda & env info
         run: |
           conda info -a
           conda list
 
+      - name: Run test script for snakemake format
+        run: bash tests/test_format/test_snakefmt.sh
+
+      - name: Run test script for snakemake lint
+        run: bash tests/test_format/test_snakemake_lint.sh
+
       - name: Run test script for snakemake rulegraph
         run: bash tests/test_create_rule_graph/test.sh
 
       - name: Run test script for snakemake DAG
         run: bash tests/test_create_dag_image/test.sh
 
+
   integration-singularity:
     needs:
-      - snakemake-graphs
+      - snakemake-graphs-format
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -86,7 +96,7 @@ jobs:
 
   integration-singularity-tempflag:
     needs:
-      - snakemake-graphs
+      - snakemake-graphs-format
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -123,7 +133,7 @@ jobs:
 
   integration-singularity-MultipleLanes:
     needs:
-      - snakemake-graphs
+      - snakemake-graphs-format
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -160,7 +170,7 @@ jobs:
 
   integration-conda:
     needs:
-      - snakemake-graphs
+      - snakemake-graphs-format
     runs-on: ubuntu-20.04
     defaults:
       run:

.gitignore

@@ -329,6 +329,7 @@ pip-selfcheck.json
 config/*
 !config/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
 !config/README.md
+!config/config.yaml
 ._*
 ._.DS_Store
 .snakemake/

config/config.yaml

@@ -0,0 +1,18 @@
+---
+  # Required fields
+  samples: "tests/input_files/samples.tsv"
+  output_dir: "results"
+  log_dir: "logs"
+  cluster_log_dir: "logs/cluster"
+  kallisto_indexes: "results/kallisto_indexes"
+  salmon_indexes: "results/salmon_indexes"
+  star_indexes: "results/star_indexes"
+  alfa_indexes: "results/alfa_indexes"
+  # Optional fields
+  rule_config: "tests/input_files/rule_config.yaml"
+  report_description: "No description provided by user"
+  report_logo: "images/logo.128px.png"
+  report_url: "https://zavolan.biozentrum.unibas.ch/"
+  author_name: "NA"
+  author_email: "NA"
+...

install/environment.dev.yml

@@ -5,6 +5,8 @@ channels:
 dependencies:
   - bedtools=2.29.2
   - biopython=1.76
+  - snakefmt
   - unzip=6.0
 
 
+

tests/test_format/test_snakefmt.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# This script is currently exiting with non-zero status.
+# This is expected behaviour though, as several parameters can't be inferred from the test files.
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
+set -u  # ensures that script exits when unset variables are used
+set -x  # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakefmt  --check ../../workflow

tests/test_format/test_snakemake_lint.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# This script is currently exiting with non-zero status.
+# This is expected behaviour though, as several parameters can't be inferred from the test files.
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
+set -u  # ensures that script exits when unset variables are used
+set -x  # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+    --snakefile="../../workflow/Snakefile" \
+    --profile="../../profiles/local-singularity" \
+    --configfile="../input_files/config.yaml" \
+    --lint

tests/test_htsinfer_workflow/test.local.sh

@@ -13,7 +13,7 @@ cleanup () {
     rm -rf .java/
     rm -rf .snakemake/
     rm -rf logs/
-    #rm -rf results/
+    rm -rf results/
     rm -rf Log.out
     cd $user_dir
     echo "Exit status: $rc"