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Merge pull request #135 from nf-core/dev
Dev -> Master for v1.9 release
2 parents 249210f + 4f51655 commit 084e5ef

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.devcontainer/devcontainer.json

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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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"remoteUser": "gitpod",
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
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"python.formatting.yapfPath": "/opt/conda/bin/yapf",
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"python.linting.flake8Path": "/opt/conda/bin/flake8",
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"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
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"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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}
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}

.gitattributes

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*.config linguist-language=nextflow
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*.nf.test linguist-language=nextflow
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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## GitHub Codespaces
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This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
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To get started:
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- Open the repo in [Codespaces](https://github.com/nf-core/fetchngs/codespaces)
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- Tools installed
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- nf-core
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- Nextflow
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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)
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- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

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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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* Nextflow version _(eg. 22.10.1)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

.github/workflows/ci.yml

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env:
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NXF_ANSI_LOG: false
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concurrency:
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group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
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cancel-in-progress: true
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jobs:
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test:
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name: Run pipeline with test data
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strategy:
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matrix:
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NXF_VER:
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- "21.10.3"
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- "22.10.1"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v2
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- uses: actions/setup-node@v3
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "::set-output name=result::pass"
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echo "result=pass" >> $GITHUB_OUTPUT
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else
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echo "::set-output name=result::fail"
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echo "result=fail" >> $GITHUB_OUTPUT
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fi
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- name: Run 'prettier --write'

.github/workflows/linting.yml

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# that the code meets the nf-core guidelines.
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on:
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push:
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branches:
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- dev
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pull_request:
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release:
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types: [published]
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EditorConfig:
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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/checkout@v3
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- uses: actions/setup-node@v2
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- uses: actions/setup-node@v3
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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Prettier:
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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/checkout@v3
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- uses: actions/setup-node@v2
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- uses: actions/setup-node@v3
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- name: Install Prettier
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run: npm install -g prettier
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PythonBlack:
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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/checkout@v3
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- name: Check code lints with Black
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uses: psf/black@stable
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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- uses: actions/setup-python@v3
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- uses: actions/setup-python@v4
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with:
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python-version: "3.7"
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architecture: "x64"
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v3
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with:
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name: linting-logs
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path: |

.github/workflows/linting_comment.yml

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- name: Get PR number
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id: pr_number
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run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
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run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
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- name: Post PR comment
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uses: marocchino/sticky-pull-request-comment@v2

.prettierignore

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email_template.html
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adaptivecard.json
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slackreport.json
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.nextflow*
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work/
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data/
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testing/
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testing*
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*.pyc
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bin/

CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [[1.9](https://github.com/nf-core/fetchngs/releases/tag/1.9)] - 2022-12-21
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### Enhancements & fixes
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- Bumped minimum Nextflow version from `21.10.3` -> `22.10.1`
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- Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
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- Added support for generating nf-core/atacseq compatible samplesheets
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- Added `--nf_core_rnaseq_strandedness` parameter to specify value for `strandedness` entry added to samplesheet created when using `--nf_core_pipeline rnaseq`. The default is `auto` which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.
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## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
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### Enhancements & fixes

CITATION.cff

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README.md

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[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
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- [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
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- [nf-core/atacseq](https://nf-co.re/atacseq/usage#samplesheet-input)
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- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
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- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
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You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
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See [usage docs](https://nf-co.re/fetchngs/1.8/usage#samplesheet-format) for more details.
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## Quick Start
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1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
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1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
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2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
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assets/slackreport.json

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{
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"attachments": [
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{
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"fallback": "Plain-text summary of the attachment.",
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"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
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"author_name": "sanger-tol/readmapping v${version} - ${runName}",
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"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
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"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
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"fields": [
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{
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"title": "Command used to launch the workflow",
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"value": "```${commandLine}```",
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"short": false
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}
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<%
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if (!success) { %>
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,
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{
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"title": "Full error message",
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"value": "```${errorReport}```",
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"short": false
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},
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{
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"title": "Pipeline configuration",
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"value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
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"short": false
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}
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<% }
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%>
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],
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"footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
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}
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]
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}

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