You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
72 lines
2.6 KiB
Plaintext
72 lines
2.6 KiB
Plaintext
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Nextflow config file for running full-size tests
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
Defines input files and everything required to run a full size pipeline test.
|
|
Use as follows:
|
|
nextflow run nf-core/taxprofiler -profile test_full,<docker/singularity> --outdir <OUTDIR>
|
|
----------------------------------------------------------------------------------------
|
|
*/
|
|
|
|
cleanup = true
|
|
|
|
params {
|
|
config_profile_name = 'Full test profile'
|
|
config_profile_description = 'Full test dataset to check pipeline function'
|
|
|
|
// Input data for full size test
|
|
input = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_full.csv'
|
|
databases = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/database_full.csv'
|
|
|
|
// Genome references
|
|
hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
|
|
|
|
save_preprocessed_reads = false
|
|
|
|
perform_shortread_qc = true
|
|
shortread_qc_mergepairs = true
|
|
perform_shortread_complexityfilter = false
|
|
save_complexityfiltered_reads = false
|
|
|
|
perform_longread_qc = true
|
|
perform_shortread_hostremoval = true
|
|
perform_longread_hostremoval = true
|
|
save_hostremoval_index = false
|
|
save_hostremoval_bam = false
|
|
save_hostremoval_unmapped = false
|
|
|
|
perform_runmerging = true
|
|
save_runmerged_reads = false
|
|
|
|
run_centrifuge = true
|
|
centrifuge_save_reads = false
|
|
|
|
run_diamond = true
|
|
|
|
run_kaiju = true
|
|
|
|
run_kraken2 = true
|
|
kraken2_save_reads = false
|
|
kraken2_save_readclassification = false
|
|
kraken2_save_minimizers = false
|
|
|
|
run_krakenuniq = true
|
|
krakenuniq_save_reads = false
|
|
krakenuniq_save_readclassifications = false
|
|
|
|
run_bracken = true
|
|
run_malt = true
|
|
malt_save_reads = false
|
|
malt_generate_megansummary = true
|
|
|
|
run_metaphlan3 = true
|
|
|
|
run_motus = true
|
|
motus_save_mgc_read_counts = true
|
|
|
|
run_profile_standardisation = true
|
|
run_krona = true
|
|
}
|
|
|
|
cleanup = true
|