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Merge pull request #755 from nf-core/dev
Release 2.10.0
2 parents 717abb8 + a1511ef commit 3f40a1b

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‎.editorconfig

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[/assets/email*]
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indent_size = unset
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# ignore python
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset

‎.github/PULL_REQUEST_TEMPLATE.md

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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/ampliseq/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/ampliseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.

‎.github/workflows/awsfulltest.yml

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types: [published]
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS full tests
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if: github.repository == 'nf-core/ampliseq'
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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/awstest.yml

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on:
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS tests
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if: github.repository == 'nf-core/ampliseq'
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runs-on: ubuntu-latest
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steps:
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# Launch workflow using Tower CLI tool action
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- name: Launch workflow via tower
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# Launch workflow using Seqera Platform CLI tool action
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/ci.yml

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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- name: Check out test data
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: ampliseq
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path: test-datasets/
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fetch-depth: 1
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheets/*.tsv; do
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sed -i "s=https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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with:
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version: "${{ matrix.NXF_VER }}"
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‎.github/workflows/download_pipeline.yml

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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Disk space cleanup
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.11"
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python-version: "3.12"
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architecture: "x64"
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- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
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with:
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --skip_qiime --outdir ./results
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
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- name: Run the downloaded pipeline (stub run not supported)
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id: run_pipeline
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if: ${{ job.steps.stub_run_pipeline.status == failure() }}
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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NXF_SINGULARITY_HOME_MOUNT: true
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --skip_qiime --outdir ./results
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

‎.github/workflows/fix-linting.yml

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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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# Install and run pre-commit
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: 3.11
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python-version: "3.12"
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‎.github/workflows/linting.yml

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pre-commit:
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Set up Python 3.11
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Set up Python 3.12
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uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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python-version: 3.11
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cache: "pip"
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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python-version: "3.12"
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
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uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
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‎.github/workflows/linting_comment.yml

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- name: Download lint results
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uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
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uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml

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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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- name: Install dependencies

‎.nf-core.yml

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https://github.com/nf-core/modules.git:
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nf-core:
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mafft: "feb29be775d9e41750180539e9a3bdce801d0609"
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nf_core_version: "2.14.1"

‎.pre-commit-config.yaml

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rev: "v3.1.0"
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- id: prettier
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additional_dependencies:
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- [email protected]
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "2.7.3"
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‎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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## nf-core/ampliseq version 2.10.0 - 2024-06-27
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### `Added`
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- [#751](https://github.com/nf-core/ampliseq/pull/751) - Added version R08-RS214 of curated GTDB 16S taxonomy: `sbdi-gtdb=R08-RS214-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
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- [#752](https://github.com/nf-core/ampliseq/pull/752) - Added version R09-RS220 of GTDB 16S taxonomy: `gtdb=R09-RS220` or `gtdb` as parameter to `--dada_ref_taxonomy`
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- [#753](https://github.com/nf-core/ampliseq/pull/753), [#756](https://github.com/nf-core/ampliseq/pull/756), [#757](https://github.com/nf-core/ampliseq/pull/757) - ANCOM-BC via QIIME2 can be used with `--ancombc`, `--ancombc_formula`, and `--ancombc_formula_reflvl`, plotting can be modified with thresholds `--ancombc_effect_size` and `--ancombc_significance`
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### `Changed`
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- [#749](https://github.com/nf-core/ampliseq/pull/749) - Create barplot also when no metadata is given
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- [#753](https://github.com/nf-core/ampliseq/pull/753) - ANCOM via QIIME2 is not run anymore by default but on request whith `--ancom`, therefore `--skip_ancom` was removed
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### `Fixed`
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- [#747](https://github.com/nf-core/ampliseq/pull/747) - Template update for nf-core/tools version 2.14.1
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- [#748](https://github.com/nf-core/ampliseq/pull/748) - Updating misleading error message and documentation
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- [#750](https://github.com/nf-core/ampliseq/pull/750) - Numbers in `overall_summary.tsv` were fixed (sometimes misleading in 2.9.0 for columns "denoised[F/R]", "merged", and "nochim")
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### `Dependencies`
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### `Removed`
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- [#753](https://github.com/nf-core/ampliseq/pull/753) - `--skip_ancom` was removed
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## nf-core/ampliseq version 2.9.0 - 2024-04-03
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### `Added`

‎CITATIONS.md

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> Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015 May 29;26:27663. doi: 10.3402/mehd.v26.27663. PMID: 26028277; PMCID: PMC4450248.
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- [ANCOM-BC](https://pubmed.ncbi.nlm.nih.gov/32665548/)
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> Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7. PMID: 32665548; PMCID: PMC7360769.
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- [Adonis](https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x) and [VEGAN](https://CRAN.R-project.org/package=vegan)
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> Marti J Anderson. A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32–46, 2001.

‎README.md

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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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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/ampliseq)
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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/ampliseq)
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[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23ampliseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/ampliseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)[![Watch on YouTube](http://img.shields.io/badge/youtube-ampliseq-FFFF00?labelColor=000000&logo=youtube)](https://youtu.be/a0VOEeAvETs)
2020

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- Phylogenetic placement ([EPA-NG](https://github.com/Pbdas/epa-ng))
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- Taxonomical classification using DADA2; alternatives are [SINTAX](https://doi.org/10.1101/074161), [Kraken2](https://doi.org/10.1186/s13059-019-1891-0), and [QIIME2](https://www.nature.com/articles/s41587-019-0209-9)
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- 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 ([QIIME2](https://www.nature.com/articles/s41587-019-0209-9))
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- Calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277))
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- Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html))
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- Pipeline QC summaries ([MultiQC](https://multiqc.info/))
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- Pipeline summary report ([R Markdown](https://github.com/rstudio/rmarkdown))
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> Adding metadata will considerably increase the output, see [metadata documentation](https://nf-co.re/ampliseq/usage#metadata).
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> [!TIP]
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> By default the taxonomic assignment will be performed with DADA2 on SILVA database, but there are various tools and databases readily available, see [taxonomic classification documentation](https://nf-co.re/ampliseq/usage#taxonomic-classification).
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> By default the taxonomic assignment will be performed with DADA2 on SILVA database, but there are various tools and databases readily available, see [taxonomic classification documentation](https://nf-co.re/ampliseq/usage#taxonomic-classification). Differential abundance testing with ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)) or ([ANCOM-BC](https://www.ncbi.nlm.nih.gov/pubmed/32665548)) when opting in.
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> [!WARNING]
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> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
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> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/ampliseq/usage) and the [parameter documentation](https://nf-co.re/ampliseq/parameters).
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‎assets/multiqc_config.yml

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.9.0" target="_blank">nf-core/ampliseq</a>
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This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.10.0" target="_blank">nf-core/ampliseq</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/ampliseq/2.9.0/docs/output" target="_blank">documentation</a>.
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<a href="https://nf-co.re/ampliseq/2.10.0/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-ampliseq-methods-description":
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order: -1000

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