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Merge branch 'feat_nftemplate' of https://github.com/CCBR/LOGAN into docker
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‎.github/CONTRIBUTING.md

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# Contributing to LOGAN
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TODO -- describe gitflow, require PRs...
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## Use pre-commit hooks
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Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.
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Install [pre-commit](https://pre-commit.com/#installation) if you haven't already,
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then run `pre-commit install` to install the hooks specified in `.pre-commit-config.yaml`.
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Pre-commit will run the hooks every time you commit.
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If you re-clone the repo, you will likely need to re-run `pre-commit install`
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as the hooks are installed to the local repo's `.git/hooks` directory.
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## Versions
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Increment the version number following semantic versioning[^1] in the `VERSION` file.
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[^1]: semantic versioning guidelines https://semver.org/
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## Changelog
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Keep the changelog up to date with all notable changes in `CHANGELOG.md`[^2].
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[^2]: changelog guidelines: https://keepachangelog.com/en/1.1.0/
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## VS code extensions
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If you use VS code, installing [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) is recommended.

‎.github/ISSUE_TEMPLATE/bug_report.yml

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name: Bug report
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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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Before you post this issue, please check the documentation:
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- [pipeline documentation: troubleshooting](https://ccbr.github.io/LOGAN/user-guide/troubleshooting/)
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- type: textarea
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id: description
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attributes:
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label: Description of the bug
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
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render: console
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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: |
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Please drag and drop any relevant files here. Create a `.zip` archive if the extension is not allowed.
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Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
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If the bug is related to a GUI, add screenshots to help explain your problem.
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- type: textarea
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id: system
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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 21.10.3)_
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* Hardware _(eg. HPC, Desktop)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity)_
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* OS _(eg. Ubuntu Linux, macOS)_
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* Version of CCBR/TOOL_NAME _(eg. 1.0, 1.8.2)_

‎.github/ISSUE_TEMPLATE/config.yml

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contact_links:
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- name: Discussions
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url: https://github.com/CCBR/LOGAN/discussions
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about: Please ask and answer questions here.

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Suggest an idea for the pipeline
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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validations:
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required: true

‎.github/PULL_REQUEST_TEMPLATE.md

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## Changes
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<!--
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Provide a summary of what is included in this Pull Request (PR).
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-->
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## Issues
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<!--
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Reference any issues related to this PR.
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If this PR fixes any issues, [use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
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when referring to the issue.
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-->
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<!--
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**Reviewers**: Use the @ feature to mention anyone responsible for reviewing/completing this request.
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-->
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## PR Checklist
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(~Strikethrough~ any points that are not applicable.)
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- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
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- ~[ ] Write unit tests for any new features, bug fixes, or other code changes.~ _testing framework not yet implemented_
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- [ ] Update docs if there are any API changes.
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- [ ] If a new nextflow process is implemented, define the process `container` and `stub`.
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- [ ] Update `CHANGELOG.md` with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

‎.github/workflows/build.yml

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name: build
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on:
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push:
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branches:
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- main
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- develop
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pull_request:
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branches:
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- main
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- develop
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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- name: Install nextflow
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uses: nf-core/setup-nextflow@v1
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools
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pip install .[dev,test]
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python -c 'from logan.src.util import chmod_bins_exec; chmod_bins_exec()'
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- name: Test stub run
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run: |
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mkdir tmp && cd tmp
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which logan
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logan init
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logan run -profile ci_stub,docker -stub

‎.github/workflows/docs.yaml

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This file was deleted.

‎.github/workflows/docs.yml

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name: mkdocs_build
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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paths:
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- "docs/**"
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env:
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actor: "41898282+github-actions[bot]"
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: git config
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run: |
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git config --local user.email "${actor}@users.noreply.github.com"
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git config --local user.name "$actor"
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- run: pip install --upgrade pip
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- run: pip install -r docs/requirements.txt
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- run: mkdocs gh-deploy --force

‎.github/workflows/projects.yml

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name: Add issues/PRs to user projects
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on:
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issues:
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types:
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- assigned
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pull_request:
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types:
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- assigned
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jobs:
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add-to-project:
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uses: CCBR/.github/.github/workflows/[email protected]
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secrets: inherit

‎.gitignore

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docs/user-guide/site/
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# Compiled class file
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*.class
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# Log file
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*.log
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# BlueJ files
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*.ctxt
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# Mobile Tools for Java (J2ME)
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.mtj.tmp/
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# Package Files #
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*.jar
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*.war
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*.nar
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*.ear
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*.zip
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*.tar.gz
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*.rar
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
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hs_err_pid*
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replay_pid*
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# nextflow
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.nextflow*
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/work*/
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/data/
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/results/
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/output/
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/params.yaml
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# python packaging
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*.pyc
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*.egg-info
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/build
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# macOS
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.DS_Store
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# code editors
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.vscode/
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*.code-workspace
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# user-specific dev files
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*KLS*
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*.Rproj
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.Rproj.user
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.Rhistory
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/submit_slurm.sh
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/tmp/

‎.pre-commit-config.yaml

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default_install_hook_types: [pre-commit, commit-msg]
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default_stages: [pre-commit]
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exclude: |
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(?x)(
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^assets/|
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^docs/.*.html
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)
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v1.2.3
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hooks:
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- id: check-added-large-files
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- id: end-of-file-fixer
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- id: trailing-whitespace
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# spell check
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.4
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hooks:
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- id: codespell
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# https://github.com/codespell-project/codespell/issues/1498
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# Python formatting
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- repo: https://github.com/psf/black
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rev: 23.7.0
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hooks:
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- id: black
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# R formatting
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- repo: https://github.com/lorenzwalthert/precommit
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rev: v0.1.2
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hooks:
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- id: style-files
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# general linting
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v2.7.1
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hooks:
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- id: prettier
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# enforce commit format
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- repo: https://github.com/compilerla/conventional-pre-commit
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rev: v2.3.0
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hooks:
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- id: conventional-pre-commit
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stages: [commit-msg]
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args: []
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- repo: https://github.com/citation-file-format/cffconvert
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rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
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hooks:
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- id: validate-cff

‎.prettierignore

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# gitignore
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.nextflow*
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work/
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data/
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results/
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.DS_Store
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*.code-workspace
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assets/*.html

‎.prettierrc

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overrides:
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- files: "*.md"
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options:
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tabWidth: 2

‎CHANGELOG.md

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# LOGAN development version
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- Python-based CLI

‎CITATION.cff

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cff-version: 1.2.0
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message: "Please cite LOGAN as below." # TODO set up Zenodo to archive your tool and assign a DOI. Or if TOOL_NAME gets published in a journal, include the citation here.
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authors: # TODO: author names should match those in pyproject.toml
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- family-names: Nousome
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given-names: Darryl
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- family-names: Sovacool
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given-names: Kelly
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orcid: https://orcid.org/0000-0003-3283-829X
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- family-names: Koparde
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given-names: Vishal
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orcid: https://orcid.org/0000-0001-8978-8495
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title: "LOGAN: whoLe genOme-sequencinG Analysis pipeliNe" # TODO: citation title should match pyproject.toml
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url: https://ccbr.github.io/LOGAN/
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repository-code: https://github.com/CCBR/LOGAN
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license: MIT

‎VERSION

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0.1.0-dev

‎workflow/resources/hg38_v0_wgs_calling_regions.hg38.bed ‎assets/hg38_v0_wgs_calling_regions.hg38.bed

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‎workflow/resources/hg38_v0_wgs_calling_regions.hg38.interval_list ‎assets/hg38_v0_wgs_calling_regions.hg38.interval_list

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‎assets/slurm_header_biowulf.sh

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#!/usr/bin/env bash
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#SBATCH --cpus-per-task=1
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#SBATCH --mem=1g
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#SBATCH --time=1-00:00:00
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#SBATCH --parsable
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#SBATCH -J "LOGAN"
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#SBATCH --mail-type=BEGIN,END,FAIL
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#SBATCH --output "log/slurm_%j.log"
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#SBATCH --output "log/slurm_%j.log"
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module load ccbrpipeliner
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module load nextflow
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NXF_SINGULARITY_CACHEDIR=/data/CCBR_Pipeliner/SIFS

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