example_config.yaml

data:
        "/location/of/RNA-seq/reads" # directory with fastq files

results_loc:
        "/location/to/save/results/" # directory where output will be saved

threads:        
        "Number of threads to use"

species:
        "human" # select "human", "mouse", or "neither" to choose the appropriate index for salmon

index:
        "/path/to/index" # set path to salmon genome index IF "neither" was chosen above

gtf:
        "/location/of/gtf/functional/annotations" # only need to specify if species is "neither"

my_samples:
        "/location/of/samples.txt" # path to tab-separated list of samples and their associated experimental condition. See "example_samples.txt". 

gzipped_reads:
        "True" #set to false if input fastq files are not gzipped

paired_reads:
        "False" # set to False if reads are single end

control:
        "WT" # name of condition from my_samples file that should act as control