biobakery · EacoChen · Sep 3, 2022 · Sep 3, 2022 · Nov 7, 2022
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,14 +1,14 @@
-We welcome feedback and issue reporting for all bioBakery tools through our [Discourse site](https://forum.biobakery.org/c/pull-request/featurepull-request/). For users that would like to directly contribute to the [tools](https://github.com/biobakery/) we are happy to field PRs to address **bug fixes**. Please note the turn around time on our end might be a bit long to field these but that does not mean we don't value the contribution! We currently **don't** accept PRs to add **new functionality** to tools but we would be happy to receive your feedback on [Discourse](https://forum.biobakery.org/c/pull-request/featurepull-request/).
-
-Also, we will make sure to attribute your contribution in our User’s manual(README.md) and in any associated paper Acknowledgements.
-
-
-## Description
-<!--- Describe your changes in detail -->
-
-## Related Issue
-<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
-<!--- Please link to the issue here: -->
-
-
-## Screenshots (if appropriate):
+We welcome feedback and issue reporting for all bioBakery tools through our [Discourse site](https://forum.biobakery.org/c/pull-request/featurepull-request/). For users that would like to directly contribute to the [tools](https://github.com/biobakery/) we are happy to field PRs to address **bug fixes**. Please note the turn around time on our end might be a bit long to field these but that does not mean we don't value the contribution! We currently **don't** accept PRs to add **new functionality** to tools but we would be happy to receive your feedback on [Discourse](https://forum.biobakery.org/c/pull-request/featurepull-request/).
+
+Also, we will make sure to attribute your contribution in our User’s manual(README.md) and in any associated paper Acknowledgements.
+
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
+<!--- Please link to the issue here: -->
+
+
+## Screenshots (if appropriate):
diff --git a/.github/workflows/auto_close_all_issues.yml b/.github/workflows/auto_close_all_issues.yml
@@ -1,16 +1,16 @@
-
-name: Auto-Close All Issues
-on:
-  issues:
-  issue_comment:
-jobs:
-  auto_close_all_issues:
-    if: ${{ !github.event.issue.pull_request }}
-    runs-on: ubuntu-latest
-    steps:
-      - uses: peter-evans/close-issue@v1
-        with:
-          comment: |
-            Thank you for creating this issue. 
-            We currently field issues through our [bioBakery Discourse Support Forum](https://forum.biobakery.org/). 
-            If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.
+
+name: Auto-Close All Issues
+on:
+  issues:
+  issue_comment:
+jobs:
+  auto_close_all_issues:
+    if: ${{ !github.event.issue.pull_request }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: peter-evans/close-issue@v1
+        with:
+          comment: |
+            Thank you for creating this issue. 
+            We currently field issues through our [bioBakery Discourse Support Forum](https://forum.biobakery.org/). 
+            If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,32 +1,32 @@
-# This is a basic workflow to help you get started with Actions
-
-name: Functional tests
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  build:
-    runs-on: ubuntu-latest
-    container:
-      image: biobakery/kneaddata:latest
-
-    steps:
-    # check out repository under $GITHUB_WORKSPACE
-    - uses: actions/checkout@v2
-
-    - name: Install
-      run: cd $GITHUB_WORKSPACE && python3 setup.py install
-
-    - name: Help
-      run: kneaddata --help
-
-    - name: Run basic test with small demo files
-      run: kneaddata --unpaired examples/demo.fastq --output output_folder -db examples/
+# This is a basic workflow to help you get started with Actions
+
+name: Functional tests
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: biobakery/kneaddata:latest
+      
+    steps:
+    # check out repository under $GITHUB_WORKSPACE
+    - uses: actions/checkout@v2
+
+    - name: Install
+      run: cd $GITHUB_WORKSPACE && python3 setup.py install
+    
+    - name: Help
+      run: kneaddata --help
+    
+    - name: Run basic test with small demo files
+      run: kneaddata --unpaired examples/demo.fastq --output output_folder -db examples/
diff --git a/LICENSE b/LICENSE
@@ -1,22 +1,22 @@
-
-The KneadData software is licensed under the MIT license.
-
-Copyright (c) 2015 Harvard School of Public Health
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+
+The KneadData software is licensed under the MIT license.
+
+Copyright (c) 2015 Harvard School of Public Health
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,13 +1,13 @@
-include LICENSE
-include readme.md
-include setup.py
-
-include examples/demo.fastq
-include examples/demo_db.1.bt2
-include examples/demo_db.2.bt2
-include examples/demo_db.3.bt2
-include examples/demo_db.4.bt2
-include examples/demo_db.rev.1.bt2
-include examples/demo_db.rev.2.bt2
-
-exclude kneaddata/adapters/*
+include LICENSE
+include readme.md
+include setup.py
+
+include examples/demo.fastq
+include examples/demo_db.1.bt2
+include examples/demo_db.2.bt2
+include examples/demo_db.3.bt2
+include examples/demo_db.4.bt2
+include examples/demo_db.rev.1.bt2
+include examples/demo_db.rev.2.bt2
+
+exclude kneaddata/adapters/*