Merged template changes and put into new branch for unique PR.

config_template/template_neat_config.yml

@@ -1,137 +1,135 @@
-## Template for gen_reads parallel
+## Template for NEAT's read-simulator (as of version 4.3.5, parallelization-friendly)
 ## Any parameter that is not required but has a default value will use the
 ## default value even if the variable is not included in the config. For
-## required items, they must be included in the config and the must be given a value.
+## required items, they must be included in the config and they must be given a value.
 ## All other items can be present or not. If present and the value is set to a single
 ## period, the variable will be treated as though it had been omitted. Please do
-## not modify this template, but instead make a copy in your working directory. Done this
-## way, you can run without even needing to declare -c.
+## not modify this template, but instead make a copy in your working directory.
+## Run with this command: neat read-simulator -c <config.yml> -o <out_dir> [-p <prefix>]
 
-# Absolute path to input reference fasta file
+# Absolute path to input reference FASTA file
 # type = string | required: yes
 reference: REQUIRED
 
-# Read length of the reads in the fastq output. Only required if @produce_fastq is set to true
-# type = int | required: no | default = 101
+# Read length of the reads in the FASTQ output. Only required if @produce_fastq is set to true
+# type = int | required: no | default = 151
 read_len: .
 
-# Average Coverage for the entire genome.
+# Average coverage for the entire genome
 # type = float | required: no | default = 10.0
 coverage: .
 
-# Absolute path to file with sequencing error model
+# Absolute path to file with sequencing error model or quality-score model.
+# Error models are typically produced by neat model-seq-err (from FASTQ/BAM-like inputs), while
+# quality-score models can be produced by neat model-qual-score (optionally fit with --markov)
 # type = string | required: no | default: <NEAT_DIR>/neat/models/defaults/default_error_model.pickle.gz
 error_model: .
 
 # Average sequencing error rate for the sequencing machine
 # type = float | required = no | must be between 0.0 and 0.3
 avg_seq_error: .
 
-# This scales the quality scores to match the desired average sequencing error rate
-# specified by avg_seq_error.
+# This scales the quality scores to match the desired average sequencing error rate specified by avg_seq_error
 # type: boolean | required = no | default = false
 rescale_qualities: .
 
-# This is the factor to add to the quality scores to get the ascii text version of the
-# score. The default follows the sanger quality offset
+# This is the factor to add to the quality scores to get the ASCII text version of the
+# score. The default follows the Sanger quality offset
 # type: int | required = no | default = 33
 quality_offset: .
 
 # Desired ploidy
 # type = int | required = no | default = 2
 ploidy: .
 
-# Absolute path to vcf file containing variants that will always be included, regardless
-# of genotype and filter. You can pre-filter your vcf for these fields before inputting it
-# if this is not the desired behavior.
+# Absolute path to VCF file containing variants that will always be included, regardless
+# of genotype and filter. You can pre-filter your VCF for these fields before inputting it
+# if this is not the desired behavior
 # type: string | required = no
 include_vcf: .
 
-# Absolute path to bed file containing reference regions that the simulation
-# should target.
+# Absolute path to BED file containing reference regions that the simulation should target
 # type = string | required = no
 target_bed: .
 
-# Scalar value for coverage in regions outside the targeted bed. Example 0.5
+# Scalar value for coverage in regions outside the targeted BED. Example: 0.5
 # would get you roughly half the coverage as the on target areas. Default is
-# 0 coverage in off-target regions. Number should be a float in decimal.
+# 0 coverage in off-target regions. Number should be a float in decimal
 # type: float | required = no | default = 0.00
 off_target_scalar: .
 
-# Absolute path to bed file containing reference regions that the simulation
-# should discard.
+# Absolute path to BED file containing reference regions that the simulation should discard
 # type = string | required = no
 discard_bed: .
 
 # Absolute path to the mutation model pickle file. Omitting this value will cause
-# NEAT to use the default model, with some standard parameters, and generally uniform biases.
+# NEAT to use the default model, with some standard parameters, and generally uniform biases
 # type: string | required = no
 mutation_model: .
 
-# Average mutation rate per base pair. Overall average is 0.001, or model default
-# Use either this value to override the mutation rate for the default or input model.
+# Average mutation rate per base pair. Overall average is 0.001, or model default.
+# Use either this value to override the mutation rate for the default or input model
 # type: float | required = no | must be between 0.0 and 0.3
 mutation_rate: .
 
-# Absolute path to a bed file with mutation rates by region.
-# Rates must be in the fourth column and be of the form "mut_rate=x.xx"
-# Rates must be between 0.00 and 0.03
+# Absolute path to a BED file with mutation rates by region.
+# Rates must be in the third column and be of the form "mut_rate=x.xx"
+# Rates must be between 0.0 and 0.3
 # type: string | required = no
 mutation_bed: .
 
-# Whether the output should be paired ended. For certain conditions (i.e., vcf only or
-# fasta only), this will be ignored. If this is true, then there must be an included fragment
+# Whether the output should be paired ended. For certain conditions (i.e., VCF only or
+# FASTA only), this will be ignored. If this is true, then there must be an included fragment
 # length model output from runner.py or a mean and standard deviation
-# by declaring values for @fragment_mean and @fragment_std_dev.
+# by declaring values for @fragment_mean and @fragment_std_dev
 # type: boolean | required = no | default = false
 paired_ended: .
 
-# Absolute path to a pickle file containing the fragment length model output
-# from runner.py.
+# Absolute path to a pickle file containing the fragment length model.
+# Typically produced by neat model-fraglen (learned from BAM alignments)
 # type: string | required = no | default: <NEAT_DIR>/neat/models/defaults/default_fraglen_model.pickle.gz
 fragment_model: .
 
-# Mean for the paired end fragment length. This only applies if paired-ended is set to true.
+# Mean for the paired-end fragment length. This only applies if paired-ended is set to true.
 # This number will form the mean for the sample distribution of the fragment lengths in the simulation
 # Note: This number is REQUIRED if paired_ended is set to true, unless a fragment length model is used.
 # type: float | required: no (unless paired-ended)
 fragment_mean: .
 
-# Standard deviation for the paired end fragment length. This only applies if paired-ended is set to true.
+# Standard deviation for the paired-end fragment length. This only applies if paired-ended is set to true.
 # This number will form the standard deviation about the mean specified above for the sample distribution
-# of the fragment lengths in the simulation.
+# of the fragment lengths in the simulation
 # Note: This number is REQUIRED if paired_ended is set to true, unless a fragment length model is used.
 # type: float | required: no (unless paired-ended)
 fragment_st_dev: .
 
-# Whether to produce the golden bam file. This file will contain the reads
+# Whether to produce the golden BAM file. This file will contain the reads
 # aligned with the exact region of the genome
 # type: boolean | required = no | default = false
 produce_bam: .
 
-# Whether to produce a vcf file containing all the mutation errors added
-# by NEAT.
+# Whether to produce a VCF file containing all the mutation errors added by NEAT
 # type: boolean | required = no | default = false
 produce_vcf: .
 
-# Whether to output the fastq(s) of the reads. This is the default output. NEAT
-# will produce 1 fastq for single ended reads or 2 fastqs for paired ended.
+# Whether to output the FASTQ(s) of the reads. This is the default output. NEAT
+# will produce 1 FASTQ for single-ended reads or 2 FASTQs for paired-ended reads
 # type: boolean | required = no | default = true
 produce_fastq: .
 
 # If set to true, this will ignore statistical models and force coverage to be
-# constant across the genome. This is considered a debugging feature.
+# constant across the genome. This is considered a debugging feature
 # type: boolean | required = no | default = false
 no_coverage_bias: .
 
 # Set an RNG seed value. Runs using identical RNG values should produce identical results
 # so things like read locations, variant positions, error positions, etc. should be the same.
-# Useful for debugging.
+# Useful for debugging
 # type: int | required = no
 rng_seed: .
 
 # Set an absolute minimum number of mutations. The program always adds at least 1 mutation.
-# Useful for very small datasets.
+# Useful for very small datasets
 # type: int | required = no
 min_mutations: .
 
@@ -141,17 +139,17 @@ min_mutations: .
 overwrite_output: .
 
 # How to split the input reference for parallelization
-# Note if threads == 1, this option has no effect.
+# Note: If threads == 1, this option has no effect.
 # type = string | required: no | default = contig | values: contig, size
 parallel_mode: .
 
 # Target block size if by = size (overlap = read_len * 2).
-# Default is 500000 when by = size. Not used for by = contig.
+# Default is 500000 when by = size. Not used for by = contig
 # type = int | required: no | default = 500000 (when by=size)
 parallel_block_size: .
 
-# Maximum number of concurrent NEAT jobs (threads or hyperthreads) to run.
-# type = int | required: no | default = all available.
+# Maximum number of concurrent NEAT jobs (threads or hyperthreads) to run
+# type = int | required: no | default = all available
 threads: .
 
 # Delete the 'splits' directory after stitching completes
@@ -160,7 +158,7 @@ threads: .
 cleanup_splits: .
 
 # Reuse existing files in '<out_dir>/splits' and skip the split step.
-# The directory must contain neat-generated files and must be in the output dir within "splits"
+# The directory must contain NEAT-generated files and must be in the output directory within "splits"
 # Note if threads == 1, this option has no effect.
 # type = bool | required: no | default = False
 reuse_splits: .