mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 18:19:54 +00:00
69 lines
2.9 KiB
Text
69 lines
2.9 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 to check pipeline 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.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 = true
|
|
run_kraken2 = true
|
|
run_bracken = true
|
|
run_malt = true
|
|
run_metaphlan3 = true
|
|
run_centrifuge = true
|
|
run_diamond = true
|
|
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
|
|
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
|
|
}
|
|
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'
|
|
}
|
|
}
|