[FEATURE] 1.8 TEMPLATE

.gitattributes

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+*.config linguist-language=nextflow

.github/CONTRIBUTING.md

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+# nf-core/proteomicslfq: Contributing Guidelines
+
+Hi there!
+Many thanks for taking an interest in improving nf-core/proteomicslfq.
+
+We try to manage the required tasks for nf-core/proteomicslfq using GitHub issues, you probably came to this page when creating one.
+Please use the pre-filled template to save time.
+
+However, don't be put off by this template - other more general issues and suggestions are welcome!
+Contributions to the code are even more welcome ;)
+
+> If you need help using or modifying nf-core/proteomicslfq then the best place to ask is on the nf-core Slack [#proteomicslfq](https://nfcore.slack.com/channels/proteomicslfq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Contribution workflow
+
+If you'd like to write some code for nf-core/proteomicslfq, the standard workflow is as follows:
+
+1. Check that there isn't already an issue about your idea in the [nf-core/proteomicslfq issues](https://github.com/nf-core/proteomicslfq/issues) to avoid duplicating work
+    * If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/proteomicslfq repository](https://github.com/nf-core/proteomicslfq) to your GitHub account
+3. Make the necessary changes / additions within your forked repository
+4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+
+If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
+
+## Tests
+
+When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
+Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
+
+There are typically two types of tests that run:
+
+### Lint Tests
+
+`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+
+If any failures or warnings are encountered, please follow the listed URL for more documentation.
+
+### Pipeline Tests
+
+Each `nf-core` pipeline should be set up with a minimal set of test-data.
+`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
+If there are any failures then the automated tests fail.
+These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+
+## Patch
+
+: warning: Only in the unlikely and regretful event of a release happening with a bug.
+
+* On your own fork, make a new branch `patch` based on `upstream/master`.
+* Fix the bug, and bump version (X.Y.Z+1).
+* A PR should be made on `master` from patch to directly this particular bug.
+
+## Getting help
+
+For further information/help, please consult the [nf-core/proteomicslfq documentation](https://nf-co.re/nf-core/proteomicslfq/docs) and don't hesitate to get in touch on the nf-core Slack [#proteomicslfq](https://nfcore.slack.com/channels/proteomicslfq) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

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+# nf-core/proteomicslfq bug report
+
+Hi there!
+
+Thanks for telling us about a problem with the pipeline.
+Please delete this text and anything that's not relevant from the template below:
+
+## Describe the bug
+
+A clear and concise description of what the bug is.
+
+## Steps to reproduce
+
+Steps to reproduce the behaviour:
+
+1. Command line: `nextflow run ...`
+2. See error: _Please provide your error message_
+
+## Expected behaviour
+
+A clear and concise description of what you expected to happen.
+
+## System
+
+- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
+- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
+- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
+- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
+
+## Nextflow Installation
+
+- Version: <!-- [e.g. 19.10.0] -->
+
+## Container engine
+
+- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- version: <!-- [e.g. 1.0.0] -->
+- Image tag: <!-- [e.g. nfcore/proteomicslfq:1.0.0] -->
+
+## Additional context
+
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+# nf-core/proteomicslfq feature request
+
+Hi there!
+
+Thanks for suggesting a new feature for the pipeline!
+Please delete this text and anything that's not relevant from the template below:
+
+## 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 about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+# nf-core/proteomicslfq pull request
+
+Many thanks for contributing to nf-core/proteomicslfq!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+
+## 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 necessary, also make a PR on the [nf-core/proteomicslfq branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/proteomicslfq)
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] Documentation in `docs` is updated
+- [ ] `CHANGELOG.md` is updated
+- [ ] `README.md` is updated
+
+**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/proteomicslfq/tree/master/.github/CONTRIBUTING.md)

.github/markdownlint.yml

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+# Markdownlint configuration file
+default: true,
+line-length: false
+no-duplicate-header:
+    siblings_only: true

.github/workflows/branch.yml

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+name: nf-core branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    steps:
+      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      - name: Check PRs
+        run: |
+          { [[ $(git remote get-url origin) == *nf-core/proteomicslfq ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]

.github/workflows/ci.yml

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+name: nf-core CI
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [push, pull_request]
+
+jobs:
+  test:
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Pull docker image
+        run: |
+          docker pull nfcore/proteomicslfq:dev && docker tag nfcore/proteomicslfq:dev nfcore/proteomicslfq:dev
+      - name: Run pipeline with test data
+        run: |
+          # TODO nf-core: You can customise CI pipeline run tests as required
+          # (eg. adding multiple test runs with different parameters)
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.github/workflows/linting.yml

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+name: nf-core linting
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+on: [push, pull_request]  
+
+jobs:
+  Markdown:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install markdownlint
+        run: |
+          npm install -g markdownlint-cli
+      - name: Run Markdownlint
+        run: |
+          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.6'
+          architecture: 'x64'
+      - name: Install pip
+        run: |
+          sudo apt install python3-pip
+          pip install --upgrade pip
+      - name: Install nf-core tools
+        run: |
+          pip install nf-core
+      - name: Run nf-core lint
+        run: |
+          nf-core lint ${GITHUB_WORKSPACE}

.gitignore

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+.nextflow*
+work/
+data/
+results/
+.DS_Store
+test*
+*.pyc

.travis.yml

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+sudo: required
+language: python
+jdk: openjdk8
+services: docker
+python: '3.6'
+cache: pip
+matrix:
+  fast_finish: true
+
+before_install:
+  # PRs to master are only ok if coming from dev branch
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ]) || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]'
+  # Pull the docker image first so the test doesn't wait for this
+  - docker pull nfcore/proteomicslfq:dev
+  # Fake the tag locally so that the pipeline runs properly
+  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
+  - docker tag nfcore/proteomicslfq:dev nfcore/proteomicslfq:dev
+
+install:
+  # Install Nextflow
+  - mkdir /tmp/nextflow && cd /tmp/nextflow
+  - wget -qO- get.nextflow.io | bash
+  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+  # Install nf-core/tools
+  - pip install --upgrade pip
+  - pip install nf-core
+  # Reset
+  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+  # Install markdownlint-cli
+  - sudo apt-get install npm && npm install -g markdownlint-cli
+
+env:
+  # Tower token is to inspect runs on https://tower.nf
+  # Use public mailbox [email protected] to log in: https://www.mailinator.com/v3/index.jsp?zone=public&query=nf-core
+  # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.10.0'  TOWER_ACCESS_TOKEN="1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1"
+   # Plus: get the latest NF version and check that it works
+  - NXF_VER=''         TOWER_ACCESS_TOKEN="1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1"
+
+
+script:
+  # Lint the pipeline code
+  - nf-core lint ${TRAVIS_BUILD_DIR}
+  # Lint the documentation
+  - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
+  # Run the pipeline with the test profile
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker -ansi-log false -name proteomicslfq-${TRAVIS_EVENT_TYPE}-${TRAVIS_PULL_REQUEST}-${TRAVIS_COMMIT:0:6}-test-description

CHANGELOG.md

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+# nf-core/proteomicslfq: Changelog
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## v1.0dev - [date]
+
+Initial release of nf-core/proteomicslfq, created with the [nf-core](http://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

Dockerfile

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+FROM nfcore/base:1.8
+LABEL authors="Julianus Pfeuffer, Lukas Heumos, Leon Bichmann, Timo Sachsenberg" \
+      description="Docker image containing all software requirements for the nf-core/proteomicslfq pipeline"
+
+# Install the conda environment
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-proteomicslfq-1.0dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-proteomicslfq-1.0dev > nf-core-proteomicslfq-1.0dev.yml

LICENSE

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+MIT License
+
+Copyright (c) Julianus Pfeuffer, Lukas Heumos, Leon Bichmann, Timo Sachsenberg
+
+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.