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Merge pull request #601 from nf-core/dev
Release 2.6.0
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‎.editorconfig

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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml,html,css,scss,js,cff}]
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[*.{md,yml,yaml,html,css,scss,js}]
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indent_size = 2
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# These files are edited and tested upstream in nf-core/modules

‎.gitattributes

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

‎.github/ISSUE_TEMPLATE/bug_report.yml

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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)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/ampliseq _(eg. 1.1, 1.5, 1.8.2)_

‎.github/PULL_REQUEST_TEMPLATE.md

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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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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)- [ ] 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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- [ ] 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 (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.

‎.github/workflows/awsfulltest.yml

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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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uses: nf-core/tower-action@v3
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uses: seqeralabs/action-tower-launch@v1
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

‎.github/workflows/awstest.yml

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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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uses: nf-core/tower-action@v3
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uses: seqeralabs/action-tower-launch@v1
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

‎.github/workflows/branch.yml

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- name: Check PRs
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if: github.repository == 'nf-core/ampliseq'
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run: |
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/ampliseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/ampliseq ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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# If the above check failed, post a comment on the PR explaining the failure
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

‎.github/workflows/ci.yml

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name: nf-core CI
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
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name: nf-core CI
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on:
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push:
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branches:
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- dev
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- "dev"
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pull_request:
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branches:
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- "dev"
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- "master"
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release:
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types: [published]
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types:
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- "published"
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env:
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NXF_ANSI_LOG: false
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NFTEST_VER: "0.7.3"
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concurrency:
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group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
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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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define_nxf_versions:
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name: Choose nextflow versions to test against depending on target branch
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.nxf_versions.outputs.matrix }}
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steps:
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- id: nxf_versions
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run: |
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if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
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echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
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else
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echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
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fi
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test:
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name: Run pipeline with test data
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# Only run on push if this is the nf-core dev branch (merged PRs)
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if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/ampliseq') }}"
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name: nf-test
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needs: define_nxf_versions
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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NXF_VER:
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- "22.10.1"
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- "latest-everything"
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NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
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tags:
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- "test"
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- "test_single"
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- "test_fasta"
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- "test_multi"
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- "test_reftaxcustom"
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- "test_doubleprimers"
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- "test_iontorrent"
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- "test_novaseq"
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- "test_pacbio_its"
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- "test_sintax"
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- "test_pplace"
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profile:
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- "docker"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v3
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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 $f
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echo "========================================"
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done;
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version: "${{ matrix.NXF_VER }}"
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- name: Run pipeline with test data
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- name: Install nf-test
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
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wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
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sudo mv nf-test /usr/local/bin/
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profiles:
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name: Run workflow profile
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# Only run on push if this is the nf-core dev branch (merged PRs)
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/ampliseq') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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# Run remaining test profiles with minimum nextflow version
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profile:
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[
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test_multi,
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test_pacbio_its,
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test_doubleprimers,
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test_iontorrent,
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test_single,
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test_fasta,
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test_reftaxcustom,
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test_novaseq,
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]
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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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- name: Install Nextflow
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- name: Run nf-test
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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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nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
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- name: Run pipeline with ${{ matrix.profile }} test profile
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- name: Output log on failure
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if: failure()
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
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sudo apt install bat > /dev/null
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batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
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#
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- name: Publish Test Report
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uses: mikepenz/action-junit-report@v3
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if: always() # always run even if the previous step fails
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with:
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report_paths: "*.xml"

‎.github/workflows/clean-up.yml

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name: "Close user-tagged issues and PRs"
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on:
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schedule:
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- cron: "0 0 * * 0" # Once a week
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jobs:
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clean-up:
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runs-on: ubuntu-latest
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permissions:
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issues: write
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pull-requests: write
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steps:
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- uses: actions/stale@v7
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with:
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stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
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stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
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close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
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days-before-stale: 30
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days-before-close: 20
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days-before-pr-close: -1
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any-of-labels: "awaiting-changes,awaiting-feedback"
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exempt-issue-labels: "WIP"
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exempt-pr-labels: "WIP"
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repo-token: "${{ secrets.GITHUB_TOKEN }}"

‎.github/workflows/linting.yml

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- uses: actions/setup-python@v4
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python-version: "3.8"
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- name: Install dependencies

‎.gitignore

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.screenrc
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ampliseq.Rproj
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results_test/*
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.nf-test/
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nf-test

‎.nf-core.yml

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repository_type: pipeline
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lint:
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files_unchanged:
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- .gitattributes
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files_exist:
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- conf/igenomes.config
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actions_ci: False

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v2.7.1"
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hooks:
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- id: prettier

‎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 2.6.0 - 2023-06-27
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### `Added`
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- [#580](https://github.com/nf-core/ampliseq/pull/580) - Add NF-TEST pipeline end-to-end tests for existing CI tests
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- [#591](https://github.com/nf-core/ampliseq/pull/591) - New version of the Unite taxonomy databases: 9.0
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- [#596](https://github.com/nf-core/ampliseq/pull/596) - New version of the PR2 taxonomy database: 5.0.0, only available with DADA2 (`--dada_ref_taxonomy`)
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- [#564](https://github.com/nf-core/ampliseq/pull/564),[#567](https://github.com/nf-core/ampliseq/pull/567),[#582](https://github.com/nf-core/ampliseq/pull/582) - Added phylogenetic placement
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- [#577](https://github.com/nf-core/ampliseq/pull/577) - Added SINTAX for taxonomic classification
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- [#575](https://github.com/nf-core/ampliseq/pull/575), [#586](https://github.com/nf-core/ampliseq/pull/586) - Added filtering step for stop codons for ASVs that are of coding regions.
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- [#597](https://github.com/nf-core/ampliseq/pull/597) - Samples with less reads than specified with `--min_read_counts` (default: 1) stop the pipeline, previously the threshold was 1KB in size.
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### `Changed`
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- [#580](https://github.com/nf-core/ampliseq/pull/580) - GitHub Actions CI - pull_request to `dev` tests with NXF_VER `latest-everything` & pull_request to `master` tests with NXF_VER `22.10.1` & `latest-everything`
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- [#563](https://github.com/nf-core/ampliseq/pull/563) - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
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- [#567](https://github.com/nf-core/ampliseq/pull/567) - Renamed `--dada_tax_agglom_min` and `--qiime_tax_agglom_min` to `--tax_agglom_min` and `--dada_tax_agglom_max` and `--qiime_tax_agglom_max` to `--tax_agglom_max`
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- [#598](https://github.com/nf-core/ampliseq/pull/598) - Updated Workflow figure with SINTAX and phylogenetic placement
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- [#599](https://github.com/nf-core/ampliseq/pull/599) - For exact species assignment (DADA2's addSpecies) PR2 taxonomy database (e.g. `--dada_ref_taxonomy pr2`) now excludes any taxa that end with " sp.".
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### `Fixed`
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- [#553](https://github.com/nf-core/ampliseq/pull/553) - Handle empty barrnap results files
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- [#554](https://github.com/nf-core/ampliseq/pull/554) - Accept taxonomy strings that contain `#`,`'`
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- [#569](https://github.com/nf-core/ampliseq/pull/569) - Make header of overall_summary.tsv consistent between input data types
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- [#573](https://github.com/nf-core/ampliseq/pull/573) - Avoid parser error for single-end data when an empty read file is detected
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- [#578](https://github.com/nf-core/ampliseq/pull/578) - Template update for nf-core/tools version 2.8, including changing `System.exit(1)` to `Nextflow.error()`
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- [#594](https://github.com/nf-core/ampliseq/pull/594) - Update metadata documentation
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- [#595](https://github.com/nf-core/ampliseq/pull/595) - Closing gaps in rarefaction depth for diversity calculations (`mindepth` in QIIME2_DIVERSITY_CORE)
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### `Dependencies`
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### `Removed`
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## nf-core/ampliseq version 2.5.0 - 2023-03-02
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### `Added`

‎CITATIONS.md

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> Sundh J, Manoharan L, Iwaszkiewicz-Eggebrecht E, Miraldo A, Andersson A, Ronquist F. COI reference sequences from BOLD DB. doi: https://doi.org/10.17044/scilifelab.20514192.v2.
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### Phylogenetic placement
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- [nf-core/phyloplace](https://nf-co.re/phyloplace)
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> Daniel Lundin. (2023). nf-core/phyloplace: First release (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.7643948
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- [HMMER](https://pubmed.ncbi.nlm.nih.gov/22039361/)
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> Eddy, Sean R. “Accelerated Profile HMM Searches.” PLoS Comput Biol 7, no. 10 (October 20, 2011): e1002195. https://doi.org/10.1371/journal.pcbi.1002195.
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- [MAFFT](https://pubmed.ncbi.nlm.nih.gov/12136088/)
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> Katoh, Kazutaka, Kazuharu Misawa, Kei‐ichi Kuma, and Takashi Miyata. “MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform.” Nucleic Acids Research 30, no. 14 (July 15, 2002): 3059–66. https://doi.org/10.1093/nar/gkf436.
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- [EPA-NG](https://pubmed.ncbi.nlm.nih.gov/30165689/)
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> Barbera, Pierre, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, and Alexandros Stamatakis. “EPA-Ng: Massively Parallel Evolutionary Placement of Genetic Sequences.” Systematic Biology 68, no. 2 (March 1, 2019): 365–69. https://doi.org/10.1093/sysbio/syy054.
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- [Gappa](https://pubmed.ncbi.nlm.nih.gov/32016344/)
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> Czech, Lucas, Pierre Barbera, and Alexandros Stamatakis. “Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data.” Bioinformatics 36, no. 10 (May 1, 2020): 3263–65. https://doi.org/10.1093/bioinformatics/btaa070.
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### Downstream analysis
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- [QIIME2](https://pubmed.ncbi.nlm.nih.gov/31341288/)
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- VSEARCH option usearch_global implements the [USEARCH](https://doi.org/10.1093/bioinformatics/btq461) algorithm
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> R.C. Edgar. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010 26(19) 2460-2461
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> Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010 26(19) 2460-2461
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- VSEARCH option sintax implements the [SINTAX](https://doi.org/10.1101/074161) algorithm
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> Edgar RC. (2016) SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, BioRxiv, 074161. Preprint.
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### Summarizing software
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