Merge branch 'master' into develop

Conflicts:
	.github/workflows/publish_pypi_test.yml
	seqnado/utils.py
	seqnado/workflow/rules/align.smk
	seqnado/workflow/snakefile_snp
	tests/test_atac.py
	tests/test_chip.py
	tests/test_rna.py
	tests/test_snp.py

.github/workflows/publish_pypi_release.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/publish_package.yml → .github/workflows/publish_pypi_test.yml

@@ -1,4 +1,4 @@
-name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+name: Publish to TestPyPI
 
 on:
   push:
@@ -29,13 +29,7 @@ jobs:
         --wheel
         --outdir dist/
     - name: Publish distribution 📦 to Test PyPI
-      if: github.ref == 'refs/heads/develop'
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.TEST_PYPI_TOKEN }}
         repository-url: https://test.pypi.org/legacy/
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -1,5 +1,5 @@
 
-![SeqNado logo](seqnado_logo.jpeg)
+![SeqNado logo](https://raw.githubusercontent.com/alsmith151/SeqNado/master/seqnado_logo.jpeg)
 # SeqNado Pipeline
 
 Pipeline based on snakemake to process ChIP-seq, ATAC-seq, RNA-seq and short read WGS data for SNP calling.

pyproject.toml

@@ -26,6 +26,7 @@ dependencies = [
     "drmaa",
     "seaborn",
     "wget",
+    "tracknado",
 ]
 
 [project.scripts]

seqnado/cli.py

@@ -40,7 +40,7 @@ def cli_design(method, files, output="design.csv"):
         from seqnado.utils import GenericFastqSamples
         design = GenericFastqSamples.from_files(files).design
     else:
-        from seqnado.utils_chipseq import ChipseqFastqSamples
+        from seqnado.utils import ChipseqFastqSamples
         design = ChipseqFastqSamples.from_files(files).design
 
     design = design.drop(columns=["paired"], errors="ignore")