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Merge pull request #1066 from nf-core/dev
`dev` -> `master` for v1.14 release
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‎.github/workflows/create-lint-wf.yml‎

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name: Create a pipeline and lint it
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on: [push, pull_request]
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# Uncomment if we need an edge release of Nextflow again
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# env: NXF_EDGE: 1
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jobs:
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MakeTestWorkflow:
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runs-on: ubuntu-latest
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env:
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NXF_VER: 21.03.0-edge
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steps:
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- uses: actions/checkout@v2
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name: Check out source-code repository
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- name: Set up Python 3.7
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- name: Set up Python 3.8
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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python-version: 3.8
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- name: Install python dependencies
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run: |

‎.github/workflows/push_dockerhub_dev.yml‎

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name: nf-core Docker push (dev)
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# This builds the docker image and pushes it to DockerHub
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# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
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on:
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push:
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branches:
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- dev
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jobs:
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push_dockerhub:
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name: Push new Docker image to Docker Hub (dev)
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runs-on: ubuntu-latest
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# Only run for the nf-core repo, for releases and merged PRs
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if: ${{ github.repository == 'nf-core/tools'}}
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env:
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DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
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DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
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strategy:
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matrix:
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image: [base, tools]
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steps:
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- name: Check out tools code
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uses: actions/checkout@v2
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- name: Build new docker image
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run: docker build --no-cache . -t nfcore/${{ matrix.image }}:dev -f ${{ matrix.image }}.Dockerfile
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- name: Push Docker image to DockerHub (dev)
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run: |
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echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
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docker push nfcore/${{ matrix.image }}:dev
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‎.github/workflows/push_dockerhub_release.yml‎

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name: nf-core Docker push (release)
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# This builds the docker image and pushes it to DockerHub
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# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
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on:
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release:
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types: [published]
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jobs:
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push_dockerhub:
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name: Push new Docker image to Docker Hub (release)
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runs-on: ubuntu-latest
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# Only run for the nf-core repo, for releases and merged PRs
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if: ${{ github.repository == 'nf-core/tools' }}
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env:
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DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
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DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
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strategy:
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matrix:
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image: [base, tools]
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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- name: Build new docker image
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run: docker build --no-cache . -t nfcore/${{ matrix.image }}:latest -f ${{ matrix.image }}.Dockerfile
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- name: Push Docker image to DockerHub (release)
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run: |
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echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
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docker push nfcore/${{ matrix.image }}:latest
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docker tag nfcore/${{ matrix.image }}:latest nf-core/${{ matrix.image }}:${{ github.event.release.tag_name }}
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docker push nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}

‎.github/workflows/pytest.yml‎

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paths:
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- "**.py"
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# Uncomment if we need an edge release of Nextflow again
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# env: NXF_EDGE: 1
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jobs:
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pytest:
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runs-on: ubuntu-latest
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env:
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NXF_VER: 21.03.0-edge
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strategy:
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matrix:
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python-version: [3.6, 3.7, 3.8]
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python-version: [3.6, 3.7, 3.8, 3.9]
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steps:
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- uses: actions/checkout@v2

‎.github/workflows/sync.yml‎

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types: [published]
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workflow_dispatch:
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env:
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NXF_VER: 21.03.0-edge
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# Uncomment if we need an edge release of Nextflow again
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# env: NXF_EDGE: 1
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jobs:
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get-pipelines:

.github/workflows/tools-api-docs.yml renamed to .github/workflows/tools-api-docs-dev.yml

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name: nf-core/tools API docs
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name: nf-core/tools dev API docs
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on:
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push:
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branches: [master, dev]
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branches: [dev]
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jobs:
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api-docs:
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- name: Build HTML docs
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run: make --directory ./docs/api html
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- name: Push docs to api-doc branch
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- name: Sync dev docs
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if: github.repository == 'nf-core/tools'
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run: |
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git checkout --orphan api-doc
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git rm -r --cache .
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rm .gitignore
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git config user.email "[email protected]"
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git config user.name "nf-core-bot"
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git add docs
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git commit --message "nf-core/tools docs build
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$GITHUB_REF - $GITHUB_SHA
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"
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git remote add nf-core https://github.com/nf-core/tools.git
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git push --force --set-upstream nf-core api-doc
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uses: SamKirkland/[email protected]
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with:
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server: ${{ secrets.ftp_server }}
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username: ${{ secrets.ftp_username}}
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password: ${{ secrets.ftp_password }}
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local-dir: './docs/api/_build/html/'
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server-dir: ${{ secrets.ftp_server_dir }}/dev/
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protocol: ${{ secrets.ftp_protocol }}
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port: ${{ secrets.ftp_port }}

‎.github/workflows/tools-api-docs-release.yml‎

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name: nf-core/tools release API docs
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on:
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release:
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types: [published]
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jobs:
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api-docs:
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name: Build & push Sphinx API docs
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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dir: [latest, $GITHUB_REF]
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steps:
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- name: Check out source-code repository
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uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Install python dependencies
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run: |
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pip install --upgrade pip
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pip install -r ./docs/api/requirements.txt
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pip install .
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- name: Build HTML docs
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run: make --directory ./docs/api html
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- name: Sync release docs
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if: github.repository == 'nf-core/tools'
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uses: SamKirkland/[email protected]
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with:
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server: ${{ secrets.ftp_server }}
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username: ${{ secrets.ftp_username}}
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password: ${{ secrets.ftp_password }}
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local-dir: './docs/api/_build/html/'
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server-dir: ${{ secrets.ftp_server_dir }}/${{ matrix.dir }}/
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protocol: ${{ secrets.ftp_protocol }}
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port: ${{ secrets.ftp_port }}

‎.gitignore‎

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.idea
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pip-wheel-metadata
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.vscode
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.*.sw?

‎CHANGELOG.md‎

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# nf-core/tools: Changelog
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## [v1.14 - Brass Chicken :chicken:](https://github.com/nf-core/tools/releases/tag/1.14) - [2021-05-11]
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### Template
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* Fixed an issue regarding explicit disabling of unused container engines [[#972](https://github.com/nf-core/tools/pull/972)]
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* Removed trailing slash from `params.igenomes_base` to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
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* Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
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* Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
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* Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
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* Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
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* Added nextflow version to quick start section and adjusted `nf-core bump-version` [[#1032](https://github.com/nf-core/tools/issues/1032)]
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* Use latest stable Nextflow version `21.04.0` for CI tests instead of the `-edge` release
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### Download
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* Fix bug in `nf-core download` where image names were getting a hyphen in `nf-core` which was breaking things.
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* Extensive new interactive prompts for all command line flags [[#1027](https://github.com/nf-core/tools/issues/1027)]
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* It is now recommended to run `nf-core download` without any cli options and follow prompts (though flags can be used to run non-interactively if you wish)
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* New helper code to set `$NXF_SINGULARITY_CACHEDIR` and add to `.bashrc` if desired [[#1027](https://github.com/nf-core/tools/issues/1027)]
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### Launch
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* Strip values from `nf-core launch` web response which are `False` and have no default in the schema [[#976](https://github.com/nf-core/tools/issues/976)]
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* Improve API caching code when polling the website, fixes noisy log message when waiting for a response [[#1029](https://github.com/nf-core/tools/issues/1029)]
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* New interactive prompts for pipeline name [[#1027](https://github.com/nf-core/tools/issues/1027)]
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### Modules
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* Added `tool_name_underscore` to the module template to allow TOOL_SUBTOOL in `main.nf` [[#1011](https://github.com/nf-core/tools/issues/1011)]
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* Added `--conda-name` flag to `nf-core modules create` command to allow sidestepping questionary [[#988](https://github.com/nf-core/tools/issues/988)]
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* Extended `nf-core modules lint` functionality to check tags in `test.yml` and to look for a entry in the `pytest_software.yml` file
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* Update `modules` commands to use new test tag format `tool/subtool`
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* New modules lint test comparing the `functions.nf` file to the template version
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* Modules installed from alternative sources are put in folders based on the name of the source repository
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### Linting
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* Fix bug in nf-core lint config skipping for the `nextflow_config` test [[#1019](https://github.com/nf-core/tools/issues/1019)]
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* New `-k`/`--key` cli option for `nf-core lint` to allow you to run only named lint tests, for faster local debugging
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* Merge markers lint test - ignore binary files, allow config to ignore specific files [[#1040](https://github.com/nf-core/tools/pull/1040)]
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* New lint test to check if all defined pipeline parameters are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)]
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* Added fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)]
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* Added pipeline schema lint checks for missing parameter description and parameters outside of groups [[#1017](https://github.com/nf-core/tools/issues/1017)]
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### General
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* Try to fix the fix for the automated sync when we submit too many PRs at once [[#970](https://github.com/nf-core/tools/issues/970)]
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* Rewrite how the tools documentation is deployed to the website, to allow multiple versions
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* Created new Docker image for the tools cli package - see installation docs for details [[#917](https://github.com/nf-core/tools/issues/917)]
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* Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only `HOME` directory
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## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]
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* Running tests twice with `nf-core modules create-test-yml` to catch unreproducible md5 sums [[#890](https://github.com/nf-core/tools/issues/890)]

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