Implement outgroup handling

[gmanthey]

Closes #21

Workflow for outgroup files:

• treat fastq files until bam the same as other files
• call only on the set of variants identified after quality/depth filter (this is the first place where vcf file is only variants and not all sites)
• merge into the all vcf file

[gmanthey]

Needs testing. (We should consider adding a testing dataset)

[gmanthey]

Tests run through now.

Some caveats/issues here:

• Currently the outgroup individuals are called parallel on each chromosome, which was tried but removed for all individuals at some point because it creates very many snakemake jobs if there are many individuals and many chromosomes (as they are multiplied), which causes the graph resolution to get slow. With few outgroup individuals, this should not cause huge issues, but might if that number gets higher.
• The point at which the outgroup individuals are added to the vcf could potentially influence filtering, as it is before the minimum depth filter on SNPs. It could be better to move merging the outgroup in to after this step?

[Copilot]

Pull request overview

Implements explicit outgroup handling in the Snakemake variant-calling pipeline so outgroup individuals are processed through mapping like other samples, then genotyped only at already-identified variant sites and merged into the final VCF.

Changes:

• Added outgroup_individuals config and updated sample parsing to optionally include/exclude outgroup individuals.
• Added per-chromosome outgroup calling and a merge step to join outgroup genotypes into chromosome VCFs before downstream filtering/merging.
• Renamed/propagated final VCF naming to include the outgroup stage (IF-OG-...) and updated example config/inputs.

Reviewed changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
workflow/Snakefile	Updates the default “all” target to the new final VCF including outgroup stage.
workflow/rules/scripts.smk	Extends get_individuals() with an include_outgroup toggle driven by config.
workflow/rules/read_processing.smk	Includes outgroup individuals in FASTQ-trimming/summary expansions.
workflow/rules/read_mapping.smk	Includes outgroup individuals in BAM generation targets.
workflow/rules/call.smk	Generalizes per-sample rename inputs via {group} and adds per-chromosome outgroup calling.
workflow/rules/filter.smk	Excludes outgroup from initial cohort filtering, then merges outgroup calls into IF VCFs and continues filtering.
workflow/rules/consensus.smk	Includes outgroup individuals in consensus FASTA generation.
example/individuals.txt	Adds an example outgroup individual FASTQ entries.
example/config.yml	Adds outgroup_individuals example configuration.
config.yml.template	Adds outgroup_individuals default configuration key.

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