millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-13 07:53:10 +00:00
Code Issues Releases Packages Activity

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

Browse source 
Add test_nothing config profile for very minimal testing
This commit is contained in:
James A. Fellows Yates 2022-08-23 15:57:52 +01:00 committed by GitHub
commit 22e03e73e3
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 53 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

47
conf/test_nothing.config Normal file
View file

@ -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
}
}

1
nextflow.config
View file

@ -208,6 +208,7 @@ profiles {
test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
}