Snakefile

from snakemake.utils import min_version
import math

min_version("7.25")

# This is the main Snakefile for the workflow. It compiles the output files
# required by the workflow. The rules used to produce the outputs are found
# in the included .smk files below:

include: "rules/0.0_angsd_pipeline.smk"
include: "rules/1.0_landscape_modeling.smk"
include: "rules/2.0_downsampling.smk"
include: "rules/3.0_bcftools_roh.smk"


all_outputs = []

all_outputs.extend(
    [
        "results/datasets/{dataset}/analyses/landscape_models/{dataset}.{ref}_all_{sites}-filts_heterozygosity-landuse.tsv",
        "results/datasets/{dataset}/analyses/landscape_models/{dataset}.{ref}_all_{sites}-filts_fst-landuse.tsv",
        "results/datasets/{dataset}/analyses/roh/bcftools/{dataset}.{ref}_all_{sites}-filts.regs.GLonly.roh",
        "results/datasets/{dataset}/analyses/roh/bcftools/{dataset}.{ref}_all_{sites}-filts.regs.calls.roh",
    ]
)

if config["downsample"]["fst"]:
    all_outputs.append(
        "results/datasets/{dataset}/analyses/fst/downsampled/{dataset}.{ref}_poppairs.downsampled_{sites}-filts.fst.global.tsv"
    )

if config["downsample"]["thetas"]:
    all_outputs.append(
        "results/datasets/{dataset}/analyses/thetas/downsampled/{dataset}.{ref}_all.downsampled_{sites}-filts.thetaMean.{win}_{step}.tsv"
    )


rule all:
    input:
        rules.angsd_all.input,
        expand(
            all_outputs,
            dataset=config["dataset"],
            ref=config["reference"]["name"],
            sites="allsites",
            win=config["params"]["thetas"]["win_size"],
            step=config["params"]["thetas"]["win_step"],
        ),
    default_target: True