Merge pull request #21 from uab-cgds-worthey/dev

DITTO using Neural Networks and SHAP

.editorconfig

@@ -0,0 +1,14 @@
+# top-most EditorConfig file
+root = true
+
+# global definitions
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+# override indents for specific filetypes
+[*.{md,yml,yaml,html,css,scss,js,cff}]
+indent_size = 2

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment used**
+OS, relevant tool versions, etc.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/pull_request_template.md

@@ -0,0 +1,22 @@
+* **Please check if the PR fulfills these requirements**
+- [ ] Tested as per the documentation and they passed
+- [ ] Docs have been added / updated (for bug fixes / features)
+
+
+* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
+
+
+
+* **What is the current behavior?** (You can also link to an open issue here)
+
+
+
+* **What is the new behavior (if this is a feature change)?**
+
+
+
+* **Does this PR introduce a breaking change?** (What changes might users need to make in their application due to this PR?)
+
+
+
+* **Other information**:

.github/workflows/linting.yml

@@ -0,0 +1,40 @@
+name: Linting- Markdown,Shell
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  markdown-linting:
+    name: Markdown lint
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: markdownlint-cli
+        uses: nosborn/github-action-markdown-cli@v3.3.0
+        with:
+          files: .
+          config_file: ".markdownlint.json"
+          # dot: false
+          # ignore_files: '".git*/**"'
+
+
+  markdown-check-links:
+    name: Markdown - checking links
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          config-file: ".markdownlint.json"
+
+  shellcheck:
+    name: Shellcheck
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@master

.gitignore

@@ -25,12 +25,7 @@ dask-worker-space/
 *.egg
 *.err
 *.out
-*.db
-*.py*.sh
-*.tsv
-*.csv
-*.gz*
-
+.DS_Store
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -51,7 +46,6 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *,cover
-*.pdf
 
 # Translations
 *.mo
@@ -72,9 +66,6 @@ target/
 # conda
 .conda
 
-# Database
-*.db
-*.rdb
 
 # Pycharm
 .idea
@@ -83,17 +74,13 @@ target/
 .ipynb_checkpoints/
 
 # exclude data from source control by default
-/data/
-cagi*/
+work
 
-#snakemake
+#snakemake or nextflow
 .snakemake/
-# data/
-variant_annotation/data/
-
-# exclude test data used for development
-to_be_deleted/test_data/data/ref
-to_be_deleted/test_data/data/reads
+.nextflow/
+.nextflow*
+report*
 
 #logs
 logs/
@@ -103,5 +90,3 @@ logs/
 
 # .java/fonts dir get created when creating fastqc conda env
 .java/
-
-/.vscode/settings.json

.markdownlint.json

@@ -0,0 +1,10 @@
+{
+    "default": true,
+    "MD007": {
+        "indent": 2
+    },
+    "MD013": {
+        "line_length": 120,
+        "tables": false
+    }
+}