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Merge pull request #111 from nf-core/minimal-test

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Add test_nothing config profile for very minimal testing
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James A. Fellows Yates 2022-08-23 15:57:52 +01:00 committed by GitHub
commit 22e03e73e3
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2 changed files with 53 additions and 5 deletions
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47
conf/test_nothing.config Normal file
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@ -0,0 +1,47 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>
----------------------------------------------------------------------------------------
*/
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others'
// 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.csv'
perform_shortread_qc = false
perform_longread_qc = false
perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
perform_runmerging = false
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_malt = false
run_metaphlan3 = false
run_centrifuge = false
run_diamond = false
run_motus = false
}
process {
withName: MALT_RUN {
maxForks = 1
}
}

11
nextflow.config
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@ -204,11 +204,12 @@ profiles {
podman.enabled = false podman.enabled = false
shifter.enabled = false shifter.enabled = false
} }
test { includeConfig 'conf/test.config' } test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' } test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' } test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
test_motus { includeConfig 'conf/test_motus.config' } test_nothing { includeConfig 'conf/test_nothing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
} }
// Load igenomes.config if required // Load igenomes.config if required