tests/testthat/test-runPipeline.R

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

library(testthat)
context("Run entire pipeline")

root <- "/gpfs_fs/vahmp/users/Fettweis/Atopobium_NTA/Wright_Collaboration/r_package/fastq2otu/"

devtools::load_all()

paired_config <- paste0(root, "inst/examples/paired/my_paired-example_config.yml")
paired_options <- yaml::yaml.load_file(paired_config)

message("Running Paired Analysis")
runPipeline(configFile = paired_config, isPaired = TRUE, getQuality = TRUE, getMergedSamples = TRUE, getDownloadedSeqs = FALSE, 
	getTrimmedAdapters = FALSE)

single_config <- paste0(root, "inst/examples/single/my_single-example_config.yml")
single_options <- yaml::yaml.load_file(single_config)

message("Running Single-End Analysis")
runPipeline(configFile = single_config, isPaired = FALSE, getQuality = TRUE, getMergedSamples = TRUE, getDownloadedSeqs = FALSE,
	getTrimmedAdapters = FALSE)