seekdeep_nanopore_general_experimental.yaml

#information about your system
sif_file_location: /nfs/jbailey5/baileyweb/bailey_share/bin/elucidator_23-07-19.sif #location of downloaded sif file
output_folder: /nfs/jbailey5/baileyweb/asimkin/tes_2017_mikalayi/4cast_nanopore/inner_primers_v2 #this is where output will go
cpus_to_use: 14 #higher CPU count speeds up runtime, uses more memory, don't exceed your system's available CPU count or available memory.
max_run_time_min: 5760 #maximum amount of time you think this job will take
max_memory_mb: 300000 #maximum amount of memory you think this job will need

#this folder should have 2 things: a folder of demultiplexed fastq files and a tab delimited file of primers
primer_plus_fastq_binding: /nfs/jbailey5/baileyweb/asimkin/tes_2017_mikalayi/4cast_nanopore/inner_primers/input_files
fastq_subfolder: fastq #name of the demultiplexed fastq folder
primer_file: inner_ids.tab.txt #name of the primer file
#If the folder of fastq files consists of soft links to fastq files, the path to
#the original fastq files should be 'bound' in the singularity image. Syntax is:
#-B original/fastq/location:original/fastq/location
#(otherwise set this variable as empty quotes '')
#caution: do not run your snakemake job from any of the direct descendant
#folders of this path - e.g. if path is /home/username/folder1/folder2/fastq, seekdeep
#can be run from /home/username/folder3 or /home/username/folder1/folder4, but
#not /home/username/folder1 or /home/username/folder1/folder2. Otherwise later
#home bindings will break.
softlink_fastq_binding: '-B /nfs/jbailey5/baileyweb/bailey_share/processed_data/nwernsma/230405_4CASTMikalayi/compiledfastqs'

#this folder should have 2 things: a folder of bowtie2 indexed genomes and a folder of gff files for each genome
genome_binding: /nfs/jbailey5/baileyweb/www/SeekDeep/data/plasmodiumData/genomes/pf
genome_subfolder: genomes #folder name of bowtie2 indexed genomes
gff_subfolder: info/gff #folder name of gff files

#these are standard parameters that a user can tweak if seekdeep is failing to retrieve accurate haplotypes
extra_gen_target_info_cmds: '--errors 2'
extra_extractor_cmds: '--extraExtractorCmds="--primerWithinStart 40
  --minLenCutOff 100"'
extra_kluster_cmds: '--extraKlusterCmds="--readLengthMinDiff 30
  --numThreads 1"'
#threshold indels below which a haplotype gets renamed as a reference.
extra_process_cluster_cmds: '--extraProcessClusterCmds="--replicateMinTotalReadCutOff 10
  --previousPop-largeBaseIndel 0.99 --previousPop-oneBaseIndel 0.99
  --previousPop-twoBaseIndel 0.99"'