Configuration

Everything is set in parameters.config. There are no command-line overrides (why).

This page sorts the parameters by what they actually affect, which is the distinction that matters most: some change your numbers, some change only where files land or how fast the run goes, and some are computed for you and should not be edited at all.

Three kinds of parameter

Parameters that change your results

Change one of these and your output changes. Step 0 records them and refuses to run if they differ from what produced your existing outputs, so that one folder never holds results from two settings.

Parameter	Effect	Page
poolSize	Individuals per pool; sets the minimum credible allele frequency	Variant Calling
diploidy	Ploidy; same threshold	Variant Calling
filterFalsePositives.sampleThreshold	Fraction of samples that must support an allele	Variant Calling
bcftools.*	Pileup and calling behaviour, including the depth cap	Variant Calling
vcffilter.minDP, vcffilter.minQUAL	Post-call depth and quality filtering	Variant Calling
samtools.filter, samtools.required, samtools.mapq	Which alignments reach the pileup	Alignment Filters
cutadapt.at_gc_error	Composition tolerance driving the clip points	Trimming & Clipping
trim_galore.quality, .autodetect, .adapter1/2	What is trimmed off the reads	Trimming & Clipping
annotate, gffFile	Whether step 8 runs and against what	Pipeline Steps
RGTags.csv	Which FASTQ pairs are one sample, and column order	Read Groups

Parameters that change speed, not answers

Safe to tune between runs. Step 0 does not track them, precisely because they cannot change a result.

Parameter	Effect	Page
threads	Cores a single task may use; drives every tool's thread count	Resources
memory	Memory ceiling for a single task	Resources
java.heapSize	JVM heap for FastQC and SnpEff	Resources
fastqc.memory	FastQC's own memory setting, in megabytes	Resources
software.*	Paths to executables, if not using the conda environment	below

Parameters that change where files go

Parameter	Effect
mainDir	Working directory — scratch, work/, symlinks
projectDir	Permanent storage — all outputs, and where your input already lives
dataSource	Subdirectory of projectDir holding the FASTQs
readPattern	Glob matching paired FASTQs; needs a {1,2} group
referenceFile, gffFile, rgTagsFile	Input filenames within projectDir
vcf.fileName	Base name for the VCFs and frequency tables

Do not edit: derived values

A large part of parameters.config is computed. The cores block derives every tool's thread count from threads; the dir block builds every path from mainDir and projectDir; filterFalsePositives.sensitivity is computed from poolSize and diploidy; snpEff.db is derived from gffFile.

Editing these by hand breaks the invariant that makes the pipeline predictable — that one number sizes the run, and one pair of paths places everything. Change the input, not the derivation.

What to decide before your first run

In rough order of how expensive it is to get wrong:

1. RGTags.csv — which FASTQ pairs share an SM. Wrong here means valid results that answer a different question, and fixing it invalidates every BAM. →
2. poolSize and diploidy — these set the frequency floor for the whole run. →
3. filterFalsePositives.sampleThreshold — decides whether alleles seen in few pools survive. The default removes them. →
4. bcftools.maxDepth — check it against the depth you sequenced for. →
5. threads — must fit the machine, or the run fails at submission. →

Changing any of items 1–4 after outputs exist means deleting those outputs. That is enforced, not advisory.

Using system tools

The software block maps each tool to a command:

software {
    samtools = 'samtools'
    bcftools = 'bcftools'
    // …
}

Replacing a command with an absolute path makes the pipeline use a system installation instead of the conda environment. This is supported but not recommended: the environment pins exact builds because Pool-seq results depend on the precise behaviour of the pileup and filtering tools, and a version mismatch will not announce itself. Use it to work around a genuine packaging problem, not as a default.