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Separate KrakenUniq test run

This commit is contained in:
James Fellows Yates 2022-12-01 10:37:14 +01:00
parent 4f6eb6fd75
commit bc98f5b80f
4 changed files with 110 additions and 0 deletions

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@ -101,3 +101,36 @@ jobs:
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
attempt_limit: 3
krakenuniq:
name: Test mOTUs with workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "21.10.3"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Show current locale
run: locale
- name: Set UTF-8 enabled locale
run: |
sudo locale-gen en_US.UTF-8
sudo update-locale LANG=en_US.UTF-8
- name: Run pipeline with test data
uses: Wandalen/wretry.action@v1.0.11
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
attempt_limit: 3

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@ -0,0 +1,72 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/
//
// Separate test as KrakenUniq database can sometimes be too big for GHA
//
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test to check mOTUs function'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_krakenuniq.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = false`
run_kraken2 = false`
run_bracken = false
run_malt = false
run_metaphlan3 = false
run_centrifuge = false
run_diamond = false
run_krakenuniq = true
run_motus = false
run_krona = true
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true
diamond_save_reads = true
}
process {
withName: MALT_RUN {
maxForks = 1
}
withName: MEGAN_RMA2INFO_TSV {
maxForks = 1
}
withName: MEGAN_RMA2INFO_KRONA {
maxForks = 1
}
withName: 'EIDO_VALIDATE' {
ext.args = '--st-index sample'
}
withName: 'EIDO_CONVERT' {
ext.args = '--st-index sample'
}
}

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@ -10,6 +10,10 @@
----------------------------------------------------------------------------------------
*/
//
// Separate test as mOTUs database download can be flaky
//
params {
config_profile_name = 'mOTUs Test profile'
config_profile_description = 'Minimal test to check mOTUs function'

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@ -242,6 +242,7 @@ profiles {
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
test_pep { includeConfig 'conf/test_pep.config' }
}