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test.config
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test.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/nascent -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
input = "${projectDir}/assets/samplesheet.csv"
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'
gtf = 's3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf'
assay_type = "GROseq"
skip_grohmm = true // FIXME Fails due to higher memory requirements
tuning_file = "${projectDir}/tests/subworkflows/local/grohmm/tuningparams_small.csv"
filter_bed = "${projectDir}/tests/samplesheets/unwanted_region.bed"
intersect_bed = "${projectDir}/tests/samplesheets/wanted_region.bed"
}