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Merge pull request #112 from nf-core/dev
PR for release 1.1.1
2 parents 57e1ee2 + e78e3fa commit f9a89f0

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‎.github/markdownlint.yml

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# Markdownlint configuration file
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default: true,
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line-length: false
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no-multiple-blanks: 0
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blanks-around-headers: false
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blanks-around-lists: false
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header-increment: false
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no-duplicate-header:
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siblings_only: true
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siblings_only: true

‎.github/workflows/branch.yml

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name: ampliseq branch protection
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# This workflow is triggered on PRs to master branch on the repository
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on:
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pull_request:
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branches:
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs are only ok if coming from an nf-core dev branch
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- uses: actions/checkout@v1
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- name: Check PRs
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run: |
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{ [[ $(git remote get-url origin) == *nf-core/ampliseq ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == patch* ]]

‎.github/workflows/ci.yml

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name: nf-core CI
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# This workflow is triggered on pushes and PRs to the repository.
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# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
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on: [push, pull_request]
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jobs:
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test:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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# Nextflow versions: check pipeline minimum and current latest
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nxf_ver: ['19.10.0', '']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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export NXF_VER=${{ matrix.nxf_ver }}
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run test
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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- name: Run multi test
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_multi,docker
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‎.github/workflows/linting.yml

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

‎.travis.yml

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before_install:
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# PRs to master are only ok if coming from dev branch
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- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
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# Pull the docker image first so the test doesn't wait for this
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- '[ $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
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- docker pull nfcore/ampliseq:dev
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# Fake the tag locally so that the pipeline runs properly
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- docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.0
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- docker tag nfcore/ampliseq:dev nfcore/ampliseq:dev
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install:
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# Install Nextflow
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- sudo apt-get install npm && npm install -g markdownlint-cli
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env:
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- NXF_VER=18.10.1 # Specify a minimum NF version that should be tested and work
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- NXF_VER='19.10.0' # Specify a minimum NF version that should be tested and work
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- NXF_VER='' # Plus: get the latest NF version and check, that it works
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script:

‎CHANGELOG.md

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# nf-core/ampliseq
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## nf-core/ampliseq version 1.1.1 - 2019
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### Pipeline Updates
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* Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10
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### Bugfixes
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* [#78](https://github.com/nf-core/ampliseq/issues/78) - All sequenced classifed to the same species
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## nf-core/ampliseq version 1.1.0 "Silver Lime Bee" - 2019
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#### Pipeline updates
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### Pipeline updates
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* [#40](https://github.com/nf-core/ampliseq/issues/40) - Added support for data originating from multiple sequencing runs
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* [#53](https://github.com/nf-core/ampliseq/issues/53) - DADA2 report is always exported
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* [#49](https://github.com/nf-core/ampliseq/issues/49) - Allowed more filtering options
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* [#63](https://github.com/nf-core/ampliseq/issues/63) - QIIME imports files by using a manifest, giving more freedom with input file names
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* [#84](https://github.com/nf-core/ampliseq/issues/84) - Add proper nf-core logo
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#### Bug fixes
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### Bug fixes
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* [#57](https://github.com/nf-core/ampliseq/issues/57) - Indicate exact regex for sequencing file names
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* [#60](https://github.com/nf-core/ampliseq/issues/60) - publish demux.qza when --untilQ2import
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## nf-core/ampliseq version 1.0.0 "Olive Steel Panda" - 2018-11-23
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Initial release of nf-core/ampliseq, created with the [nf-core](http://nf-co.re/) template.

‎Dockerfile

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FROM nfcore/base
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FROM nfcore/base:1.7
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LABEL description="Docker image containing all requirements for nf-core/ampliseq pipeline"
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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ENV PATH /opt/conda/envs/nf-core-ampliseq-1.1.0/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-ampliseq-dev/bin:$PATH
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## Required to build the container properly
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RUN mkdir -p /root/.config/matplotlib
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RUN echo "backend : Agg" > /root/.config/matplotlib/matplotlibrc
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## Don't recache on each execution, do that once per build process
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RUN qiime dev refresh-cache
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‎README.md

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# ![nf-core/ampliseq](docs/images/nfcore-ampliseq_logo.png)
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[![Build Status](https://travis-ci.com/nf-core/ampliseq.svg?branch=master)](https://travis-ci.com/nf-core/ampliseq)[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A518.10.1-brightgreen.svg)](https://www.nextflow.io/)
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[![Build Status](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)
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[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
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[![Docker](https://img.shields.io/docker/automated/nfcore/ampliseq.svg)](https://hub.docker.com/r/nfcore/ampliseq)
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![Singularity Container available](
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https://img.shields.io/badge/singularity-available-7E4C74.svg)
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[![DOI](https://zenodo.org/badge/150448201.svg)](https://zenodo.org/badge/latestdoi/150448201)
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### Introduction
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## Introduction
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**nfcore/ampliseq** is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.
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The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)), trims primer sequences from the reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)), imports data into [QIIME2](https://qiime2.org/), generates amplicon sequencing variants (ASV, [DADA2](https://www.nature.com/articles/nmeth.3869)), classifies features against the [SILVA](https://www.arb-silva.de/) [v132](https://www.arb-silva.de/documentation/release-132/) database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)). See the [output documentation](docs/output.md) for more details of the results.
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The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)), trims primer sequences from the reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)), imports data into [QIIME2](https://www.nature.com/articles/s41587-019-0209-9), generates amplicon sequencing variants (ASV, [DADA2](https://www.nature.com/articles/nmeth.3869)), classifies features against the [SILVA](https://www.arb-silva.de/) [v132](https://www.arb-silva.de/documentation/release-132/) database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)). See the [output documentation](docs/output.md) for more details of the results.
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The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
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‎conf/base.config

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memory = { check_max (16.GB * task.attempt, 'memory' ) }
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time = { check_max (2.h * task.attempt, 'time' ) }
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}
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withName: alpha_diversity {
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errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
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}
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}
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params {

‎conf/test.config

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// Input data
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FW_primer = "GTGYCAGCMGCCGCGGTAA"
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RV_primer = "GGACTACNVGGGTWTCTAAT"
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classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza"
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classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-gg_13_8-85-qiime2_2019.7-classifier.qza"
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metadata = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/Metadata.tsv"
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outdir = "./results"
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temp_dir = "./results/tmp_dir"

‎conf/test_multi.config

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// Input data
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FW_primer = "GTGYCAGCMGCCGCGGTAA"
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RV_primer = "GGACTACNVGGGTWTCTAAT"
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classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza"
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classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-gg_13_8-85-qiime2_2019.7-classifier.qza"
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metadata = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/Metadata_multi.tsv"
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outdir = "./results"
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temp_dir = "./results/tmp_dir"

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