wrangle_data.yaml

#folder where your output will go
output_folder: /nfs/jbailey5/baileyweb/asimkin/miptools/miptools_tutorial/test-data/wrangler3

#subfolder where wrangler analysis files will go
analysis_dir: snakemake_mouse

#number of umis to include for each mip (higher expressed umis have a higher
#chance of being included than lower expressed ones)
umi_threshold: 200000000000000000

#how many CPUs (or threads) to use in parallel
cpu_count: 10

#location of sample sheet
input_sample_sheet: /nfs/jbailey5/baileyweb/asimkin/miptools/miptools_tutorial/test-data/test_data/sample_list.tsv

#location of project resources
project_resources: /nfs/jbailey5/baileyweb/asimkin/miptools/miptools_tutorial/test-data/DR1_project_resources

#location of input fastq file
fastq_dir: /nfs/jbailey5/baileyweb/asimkin/miptools/miptools_tutorial/test-data/test_data/fastq

#location of sif file to use
miptools_sif: /nfs/jbailey5/baileyweb/bailey_share/bin/miptools_dev_23-07-18.sif

#probe sets to analyze from the sample sheet
probe_sets_used: DR1

#sample sets to analyze from the sample sheet
sample_sets_used: JJJ

#a name for the output files
experiment_id: 230824

#minimum size of haplotype to consider
min_capture_length: 30