config_template.yaml

---
#############################
#### REQUIRED PARAMETERS ####
#############################

# All paths are relative to the current working directory unless noted otherwise

samples: path/to/samples_table.tsv

#### GENOME RESOURCES #####

# All genome resources have to match the source/organism
# of all samples in the sample table

genome_file: path/to/gzipped/ensembl/genome.fa.gz
gtf_file: path/to/gzipped/ensembl/gene_annotations.gtf.gz
mirna_file: path/to/unzipped/mirbase/mirna_annotations.gff3
bed_file: path/to/pileups/genomic_regions.bed

# Tab-separated mappings table between UCSC (column 1)
# and Ensembl (coulm 2) chromosome names 
# Available at: https://github.com/dpryan79/ChromosomeMappings
map_chr_file: path/to/ucsc_ensembl_mappings.tsv


###############################
#### "OPTIONAL" PARAMETERS ####
###############################

# The below parameters only need to be changed if the default behavior of
# MIRFLOWZ is to be changed; however, they still need to be present!

#### DIRECTORIES ####

output_dir: results/
pileups_dir: results/pileups
intermediates_dir: results/intermediates
local_log: logs/local/
cluster_log: logs/cluster/
scripts_dir: ../scripts/

#### PROCESSING PARAMETERS #### 

# annotation modifications
extension: 6 # extension of the mature miRNA start and end coordinates in bp

# quality filter
q_value: 10 # Q (Phred) score; minimum quality score to keep
p_value: 50 # minimum % of bases that must have Q quality

# adapter removal
error_rate: 0.1 # fraction of allowed errors
minimum_length: 15 # discard processed reads shorter than the indicated length
overlap: 3 # minimum overlap length of adapter and read to trim the bases
max_n: 0 # discard reads containing more than the indicated number of N bases

# mapping
max_length_reads: 30 # maximum length of processed reads to map with oligomap
nh: 100 # discard reads with more mappings than the indicated number

#### QUANTIFICATION PARAMETERS ####

# Types of miRNAs to quantify
# Remove miRNA types you are not interested in.
# If 'isomir' and 'mirna' are both in the list, a single table with both types
# is made.
mir_list: ['isomir', 'mirna', 'pri-mir']

#### ASCII-STYLE ALIGNMENT PILEUPS PARAMETERS ####

# Dictionary with the list of library names to aggregate when performing the
# pileups as values and the condition as keys. Library names must match the
# ones in the samples table `sample` column. The dictionary keys will be used
# as the pileup's output directory name.
# e.g. lib_dict: {"group_A": ["lib_1", "lib_3"], "group_B": ["lib_2"]}
#
# Leave as an empty dictionary if no pileups are desired.
lib_dict: {}
...