PIGA/Snakefile at main · JianYang-Lab/PIGA · GitHub

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shell.prefix = ['set -e']

import os


samples_list, sex_list, sample_sex_dict = [], [], {}
with open(config['samples']) as f:
    for line in f:
        if not line.strip():
            continue

        sample = line.strip().split()[0]
        sex = line.strip().split()[1]

        samples_list.append(sample)
        sex_list.append(sex)
        sample_sex_dict[sample] = sex
config['sex'] = sample_sex_dict

wildcard_constraints:
    sample='|'.join(samples_list)


#load the included snakemake files.
include: "rules/utils.smk"


Call_SR_SNV = config.get("Call_SR_SNV", False)
Call_LR_SNV = config.get("Call_LR_SNV", False)
Merge_SNV = config.get("Merge_SNV", False)
Phase_SNV = config.get("Phase_SNV", False)
Generate_Personal_Reference = config.get("Generate_Personal_Reference", False)
Draft_Assembly = config.get("Draft_Assembly", False)
Construct_Pangenome = config.get("Construct_Pangenome", False)
Simplify_Pangenome = config.get("Simplify_Pangenome", False)
Merge_Pangenome = config.get("Merge_Pangenome", False)
Infer_Diploid_Path = config.get("Infer_Diploid_Path", False)


if Call_SR_SNV:

    include: "rules/call_sr_snv.smk"
    rule all:
        input:
            rules.all_call_sr_snv.input

elif Call_LR_SNV:

    include: "rules/call_lr_snv.smk"
    rule all:
        input:
            rules.all_call_lr_snv.input

elif Merge_SNV:

    include: "rules/merge_snv.smk"
    rule all:
        input:
            rules.all_merge_snv.input

elif Phase_SNV:

    include: "rules/phase_snv.smk"
    rule all:
        input:
            rules.all_phase_snv.input

elif Generate_Personal_Reference:

    include: "rules/generate_personal_reference.smk"
    rule all:
        input:
            rules.all_generate_personal_reference.input

elif Draft_Assembly:

    include: "rules/draft_assembly.smk"
    rule all:
        input:
            rules.all_draft_assembly.input

elif Construct_Pangenome:

    include: "rules/construct_pangenome.smk"
    rule all:
        input:
            rules.all_construct_pangenome.input

elif Simplify_Pangenome:

    include: "rules/simplify_pangenome.smk"
    rule all:
        input:
            rules.all_simplify_pangenome.input

elif Merge_Pangenome:

    include: "rules/merge_pangenome.smk"
    rule all:
        input:
            rules.all_merge_pangenome.input

elif Infer_Diploid_Path:

    include: "rules/infer_diploid_path.smk"
    rule all:
        input:
            rules.all_infer_diploid_path.input
else:

    include: "rules/call_sr_snv.smk"
    include: "rules/call_lr_snv.smk"
    include: "rules/merge_snv.smk"
    include: "rules/phase_snv.smk"
    include: "rules/generate_personal_reference.smk"
    include: "rules/draft_assembly.smk"
    include: "rules/construct_pangenome.smk"
    include: "rules/simplify_pangenome.smk"
    include: "rules/merge_pangenome.smk"
    include: "rules/infer_diploid_path.smk"
    rule all:
        input:
            rules.all_infer_diploid_path.input


#allow_missing=True