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Separate KrakenUniq test run
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4 changed files with 110 additions and 0 deletions
33
.github/workflows/ci.yml
vendored
33
.github/workflows/ci.yml
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@ -101,3 +101,36 @@ jobs:
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with:
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command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
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attempt_limit: 3
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krakenuniq:
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name: Test mOTUs with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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NXF_VER:
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- "21.10.3"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Show current locale
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run: locale
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- name: Set UTF-8 enabled locale
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run: |
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sudo locale-gen en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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- name: Run pipeline with test data
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uses: Wandalen/wretry.action@v1.0.11
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with:
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command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
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attempt_limit: 3
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72
conf/test_krakenuniq.config
Normal file
72
conf/test_krakenuniq.config
Normal file
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@ -0,0 +1,72 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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//
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// Separate test as KrakenUniq database can sometimes be too big for GHA
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//
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test to check mOTUs function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_krakenuniq.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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shortread_qc_mergepairs = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_runmerging = true
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = false`
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run_kraken2 = false`
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run_bracken = false
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run_malt = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_diamond = false
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run_krakenuniq = true
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run_motus = false
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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}
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withName: MEGAN_RMA2INFO_TSV {
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maxForks = 1
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}
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withName: MEGAN_RMA2INFO_KRONA {
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maxForks = 1
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -10,6 +10,10 @@
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----------------------------------------------------------------------------------------
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*/
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//
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// Separate test as mOTUs database download can be flaky
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//
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params {
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config_profile_name = 'mOTUs Test profile'
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config_profile_description = 'Minimal test to check mOTUs function'
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@ -242,6 +242,7 @@ profiles {
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_nothing { includeConfig 'conf/test_nothing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
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test_pep { includeConfig 'conf/test_pep.config' }
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}
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