KwanLab · evanroyrees · Feb 8, 2022 · Nov 19, 2019 · Nov 19, 2019 · Jan 22, 2020
diff --git a/.condarc b/.condarc
@@ -0,0 +1,6 @@
+channels:
+    - defaults
+    - bioconda
+    - conda-forge
+show_channels_urls: True
+default_threads: 6
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,23 @@
+# Ignore some root directory files unnecessarily expanding image (and context) size
+.git
+docs
+autometa.mf
+MANIFEST.in
+LICENSE.txt
+meta.yaml
+# Ignore tests related files
+pytest.ini
+tests
+make_test_data.py
+# Ignore nextflow related files
+autometa.nf
+nextflow
+nextflow.config
+pipeline_info
+# Ignore any files/directories built from source
+dist
+Autometa.egg-info
+# Ignore databases
+autometa/databases
+!autometa/databases/markers
+/work
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,3 @@
+*.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
@@ -0,0 +1,6 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config
+    publish: True
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,5 +1,4 @@
-Contributing Guidelines
-=======================
+# Contributing Guidelines
 
 First off, thanks for taking the time to contribute! :clap::+1::tada:
 
@@ -8,40 +7,75 @@ First off, thanks for taking the time to contribute! :clap::+1::tada:
 [Contributing Code](#contributing-code)
 
 [How Can I Contribute?](#how-can-i-contribute)
-  * [Reporting Bugs](#reporting-bugs)
-  * [Suggesting Enhancements](#suggesting-enhancements)
-  * [Submitting pull requests](#pull-requests)
+
+- [Reporting Bugs](#reporting-bugs)
+- [Suggesting Enhancements](#suggesting-enhancements)
+- [Submitting pull requests](#pull-requests)
 
 [Style guides](#style-guides)
-  * [git commit messages](#git-commit-messages)
-  * [documentation style guide](#documentation-style-guide)
-  * [python style guide](#python-style-guide)
 
-### Contributing Code
+- [git commit messages](#git-commit-messages)
+- [documentation style guide](#documentation-style-guide)
+- [python style guide](#python-style-guide)
 
-1. Fork the KwanLab Autometa repository. You can do this [here](https://github.com/KwanLab/Autometa).
-2. <details><summary>Add the KwanLab as the upstream remote.</summary><code>
-    git remote add upstream https://github.com/KwanLab/Autometa.git</code></details>
-3. Update your local repository with the most recent updates from the Kwan Lab.
-    - <details><summary>Update your local repository.</summary><code>git pull upstream master</code></details>
-    - <details><summary>Push changes to update your remote repository.</summary><code>git push origin master</code></details>
-4. <details><summary>Check out a branch corresponding to the feature you wish to add.</summary><code>git checkout -b your-new-feature master</code></details>
-5. File an issue with the feature you plan on adding. This will open a channel of
-communication with the core developers. See [suggesting enhancements](#suggesting-enhancements) for details.
-6. Submit a pull request! To submit a pull request - see [instructions below](#pull-requests).
+### Contributing Code
 
+1. File an issue with the feature you plan on adding. This will open a channel of
+   communication with the core developers. See [suggesting enhancements](#suggesting-enhancements) for details.
+
+2. <details>
+      <summary>Fork the KwanLab Autometa repository.</summary><summary> You can do this here: https://github.com/KwanLab/Autometa</summary>
+      <summary>Clone your fork.</summary><code>git clone https://github.com/YourUserName/Autometa.git</code>
+      <summary>Then navigate to the Autometa directory.</summary><code>cd Autometa</code>
+   </details>
+
+3. <details>
+      <summary>Add the KwanLab as the upstream remote.</summary>
+      <code>git remote add upstream https://github.com/KwanLab/Autometa.git</code>
+   </details>
+
+4. <details>
+      <summary>Check out a branch respective to the contribution you plan to make.</summary>
+      <summary>Check out the <code>hotfix</code> branch from <code>master</code> if fixing a bug.</summary><code>git checkout -b hotfix master</code>
+      <summary>If adding a feature, check out a branch corresponding to the feature you wish to add from <code>dev</code>.</summary>
+      <summary> First checkout dev</summary><code>git checkout dev</code>
+      <summary>Then checkout your feature</summary><code>git checkout -b your-new-feature dev</code>
+   </details>
+
+5. <details>
+      <summary>Update your local repository with the most recent updates from the Kwan Lab.</summary>
+      <summary>Update the <code>master</code> branch if fixing a bug.</summary><code>git pull upstream master</code>
+      <summary>Otherwise update <code>your-new-feature</code> branch with <code>dev</code> and resolve any merge conflicts.</summary><code>git pull upstream dev</code>
+      <summary><b>Note: Whenver you return to the feature, make sure to pull from upstream to ensure you are working on the most up-to-date code.</b></summary>
+      <summary>Update your local repository with any changes from the Kwan Lab.</summary>
+      <code>git push origin master</code>
+      <br>
+      or
+      <br>
+      <code>git push origin dev</code>
+      <br>
+      <code>git push origin your-new-feature</code>
+   </details>
+
+6. <details>
+      <summary>Ensure pre-commit hooks are installed.</summary>
+      <code>conda install -c conda-forge pre-commit</code>
+      <br>
+      <code>pre-commit install</code>
+   </details>
+
+7. Submit a pull request! To submit a pull request - see [instructions below](#pull-requests).
 
 ## How can I contribute?
 
 ### Reporting Bugs
 
 > **Note:** If you find a **Closed** issue that seems like it is the same thing
-that you're experiencing, open a new issue and include a link to the original
-issue in the body of your new one.
+> that you're experiencing, open a new issue and include a link to the original
+> issue in the body of your new one.
 
 When submitting a bug report, please follow the bug report [template](https://github.com/KwanLab/Autometa/blob/master/.github/ISSUE_TEMPLATE/bug_report.md).
 
-
 ### Suggesting Enhancements
 
 Feature requests may be submitted by creating a new issue. When creating this issue, please follow [this template](https://github.com/KwanLab/Autometa/blob/master/.github/ISSUE_TEMPLATE/feature_request.md). After your feature request has been submitted, a maintainer will respond with a determination of whether this feature is appropriate for Autometa. If a maintainer has not responded within a reasonable time period, you can notify the Autometa team. See [notifying the team](#notifying-the-team) for details.
@@ -58,9 +92,10 @@ Please follow these steps to have your contribution considered by the maintainer
 
 1. Follow all instructions in respective [bug_fix](https://github.com/KwanLab/Autometa/blob/master/.github/PULL_REQUEST_TEMPLATE/bug_fix.md) or [feature_change](https://github.com/KwanLab/Autometa/blob/master/.github/PULL_REQUEST_TEMPLATE/feature_change.md) templates.
 2. Follow the [style guides](#style-guides).
->Note: If writing a new file, a template.py file is provided within the autometa code base to help follow the structure requested by the Autometa team.
-Please copy and rename this file before you start writing your feature.
-The template file may be found [here](https://github.com/KwanLab/Autometa/blob/dev/docs/template.py), or you may find it within your cloned repository under 'Autometa/docs/template.py'
+
+   > Note: If writing a new file, a `template.py` file is provided within the autometa code base to help follow the structure requested by the Autometa team.
+   > Please copy and rename this file before you start writing your feature.
+   > The template file may be found [here](https://github.com/KwanLab/Autometa/blob/dev/docs/template.py), or you may find it within your cloned repository under 'Autometa/docs/template.py'
 
 3. After you submit your pull request, verify that all [status checks](https://help.github.com/articles/about-status-checks/) are passing. <details><summary>What if the status checks are failing?</summary>If a status check is failing, and you believe that the failure is unrelated to your change, please leave a comment on the pull request explaining why you believe the failure is unrelated. A maintainer will re-run the status check for you. If we conclude that the failure was a false positive, then we will open an issue to track that problem with our status check suite.</details>
 
@@ -70,43 +105,43 @@ While the above must be satisfied, additional prerequisites may be present, depe
 
 ### Git Commit Messages
 
-* Use the present tense ("Add feature" not "Added feature")
-* Limit the first line to 72 characters or less
-* Reference issues and pull requests liberally after the first line
-* Consider starting the commit message with an applicable emoji:
-    * :art: `:art:` when improving the format/structure of the code
-    * :racehorse: `:racehorse:` when improving performance
-    * :memo: `:memo:` when writing docs
-    * :penguin: `:penguin:` when fixing something on Linux
-    * :apple: `:apple:` when fixing something on macOS
-    * :bug: `:bug:` when fixing a bug
-    * :fire: `:fire:` when removing code or files
-    * :green_heart: `:green_heart:` when fixing the CI build
-    * :white_check_mark: `:white_check_mark:` when adding tests
-    * :arrow_up: `:arrow_up:` when upgrading dependencies
-    * :arrow_down: `:arrow_down:` when downgrading dependencies
-    * :whale: `:whale:` when fixing the docker build
+- Use the present tense ("Add feature" not "Added feature")
+- Limit the first line to 72 characters or less
+- Reference issues and pull requests liberally after the first line
+- Consider starting the commit message with an applicable emoji:
+  - :art: `:art:` when improving the format/structure of the code
+  - :racehorse: `:racehorse:` when improving performance
+  - :memo: `:memo:` when writing docs
+  - :penguin: `:penguin:` when fixing something on Linux
+  - :apple: `:apple:` when fixing something on macOS
+  - :bug: `:bug:` when fixing a bug
+  - :fire: `:fire:` when removing code or files
+  - :green_heart: `:green_heart:` when fixing the CI build
+  - :white_check_mark: `:white_check_mark:` when adding tests
+  - :arrow_up: `:arrow_up:` when upgrading dependencies
+  - :arrow_down: `:arrow_down:` when downgrading dependencies
 
 ### Documentation Style Guide
 
 Documentation is hosted on reathedocs.org which uses sphinx, a python documentation generator. Therefore a common syntax for
 documenting files within the source code is required. The Autometa team follows numpy syntax to automate as much of the documentation build as possible.
 
-* Numpy documentation [style guide](https://numpydoc.readthedocs.io/en/latest/format.html)
-* Sphinx restructured text [style guide](http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#paragraphs)
+- Numpy documentation [style guide](https://numpydoc.readthedocs.io/en/latest/format.html)
+- Sphinx restructured text [style guide](http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#paragraphs)
 
 ### Python Style Guide
 
-When in doubt, you may reference:
-
-* google's python [style guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md)
-* [PEP8](https://www.python.org/dev/peps/pep-0008/)
+We have moved all development to using the [black](black.readthedocs.io) formatter and run
+[pre-commit](https://pre-commit.com/) hooks with black such that all of the fuss with formatting according to code
+specifications can be ignored! When first cloning the repository, you should first install
+pre-commit and run `pre-commit install`. This will ensure any commits you make will be
+formatted appropriately.
 
 ### Notifying the Team
 
 You may notify the Autometa team corresponding to the respective update/bug by mentioning them in a comment within your issue or pull request.
 
->Note: Please only use <code>@KwanLab/autometa</code> if you receive no response from any of the other teams below.
+> Note: Please only use <code>@KwanLab/autometa</code> if you receive no response from any of the other teams below.
 
 | Team                                   | Area of Development                       |
 | -------------------------------------- | ----------------------------------------- |

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -35,10 +35,9 @@ your issue, and it is not provided (in a timely manner), your issue may be close
 
 ## Environment Information
 
-<details>
+<details><summary><code>autometa-configure --dryrun --debug</code></summary><p>
 
-<!-- between the ticks below, please place in any system environment information. 
-If you are using conda try `conda list -n <your environment>` and paste below. -->
+<!-- between the ticks below, paste the output of 'autometa-configure --dryrun --debug' -->
 
 ```bash
 
@@ -48,9 +47,19 @@ If you are using conda try `conda list -n <your environment>` and paste below. -
 
 ## Run Information
 
-<details><summary>contents of <code>run_autometa.log</code></summary><p>
-<!-- between the ticks below, paste the information from your run_autometa.log file
-'cat </path/to/your/run_autometa.log file>' -->
+<details><summary>contents of <code>parameters.config</code></summary><p>
+<!-- between the ticks below, paste the information from your input config file
+'cat </path/to/your/input/parameters.config>' -->
+
+```bash
+
+```
+
+</p></details>
+
+<details><summary>contents of <code>.nextflow.log</code></summary><p>
+<!-- between the ticks below, paste the information from the autometa written config file
+within the output directory of the autometa run. 'cat </path/to/your/outdir/metagenome.config>' -->
 
 ```bash
 

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #autometa channel"
+    url: https://nfcore.slack.com/channels/autometa
+    about: Discussion about the nf-core/autometa pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,9 +1,6 @@
 ---
 name: Feature request
 about: Suggest an idea for this project and how it might help the community
-title: ''
-labels: enhancement
-assignees: ''
 
 ---
 

diff --git a/.github/ISSUE_TEMPLATE/support_request.md b/.github/ISSUE_TEMPLATE/support_request.md
@@ -1,10 +1,6 @@
 ---
 name: Support request
 about: Need clarification on a few scripts or the pipeline in general? Ask us!
-title: ''
-labels: help wanted
-assignees: ''
-
 ---
 
 <!--
@@ -17,7 +13,7 @@ Autometa here.
 ### User checklist
 
 - [ ] Are you using the latest release?
-- [ ] Are you using python 2.7?
+- [ ] Are you using python 3?
 - [ ] Did you check previous issues to see if this has already been mentioned?
 - [ ] Are you using a Mac or Linux machine?
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,26 @@
+<!--
+# nf-core/autometa pull request
+
+Many thanks for contributing to nf-core/autometa!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/autometa/tree/master/.github/CONTRIBUTING.md)
+-->
+<!-- markdownlint-disable ul-indent -->
+
+## PR checklist
+
+- [ ] This comment contains a description of changes (with reason).
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/autometa/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/autometa _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Usage Documentation in `docs/usage.md` is updated.
+- [ ] Output Documentation in `docs/output.md` is updated.
+- [ ] `CHANGELOG.md` is updated.
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).
diff --git a/.github/PULL_REQUEST_TEMPLATE/bug_fix.md b/.github/PULL_REQUEST_TEMPLATE/bug_fix.md
@@ -1,7 +1,5 @@
 ### Requirements for Applying a Bug Fix
 
-<!-- This pull request should be compared against the branch where the bug was encountered. Make sure you are submitting the PR accordingly. -->
-
 * Fill out the template below. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion.
 * The pull request must update the test suite to exercise the updated functionality. For guidance, please see [writing tests](https://autometa.readthedocs.io/writing-tests).
 * After you create the pull request, all status checks must be passed before a maintainer reviews your contribution. For more details, please see <https://github.com/KwanLab/Autometa/tree/master/.github/CONTRIBUTING.md#pull-requests>.

diff --git a/.github/PULL_REQUEST_TEMPLATE/feature_change.md b/.github/PULL_REQUEST_TEMPLATE/feature_change.md
@@ -1,9 +1,5 @@
 ### Requirements for Adding, Changing, or Removing a Feature
 
-<!-- This pull request should be compared against the `dev` branch as new
-features need to be more comprehensively tested before being released into production.
--->
-
 * Fill out the template below. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion.
 * The pull request must update the test suite to exercise the updated functionality. For guidance, please see [writing tests](https://autometa.readthedocs.io/writing-tests).
 * After you create the pull request, all status checks must be passed before a maintainer reviews your contribution. For more details, please see <https://github.com/KwanLab/Autometa/tree/master/.github/CONTRIBUTING.md#pull-requests>.