mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-29 11:09:55 +00:00
47 lines
2.2 KiB
Text
47 lines
2.2 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
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
|
|
}
|
|
}
|