Snakefile

configfile: '/project/haplotyping/nico/scripts/diploid_assembly_sv_detection/config.yml'
workdir: '/project/haplotyping/nico/analysis/DiploidAssembly/'

include: 'smk_include/utils.smk'
include: 'smk_include/01_squashed_assembly.smk'
include: 'smk_include/02_strandseq_mapping.smk'
include: 'smk_include/03_cluster_assembly.smk'
include: 'smk_include/04_map_to_assembly.smk'
include: 'smk_include/05_variant_calling.smk'
include: 'smk_include/06_haplotyping.smk'
include: 'smk_include/07_diploid_assembly.smk'
include: 'smk_include/08_polish_assembly.smk'
include: 'smk_include/09_eval_assembly.smk'


rule build_squashed_assembly:
    input:
        'references/assemblies/{sample}_sqa-wtdbg-100kb.fasta'
    output:
        '{sample}.build_squahsed_assembly.complete'
    shell:
        'echo {output}'


rule strandseq_mapping:
    input:
        collect_strandseq_alignments
    output:
        '{reference}.strandseq_mapping.complete'
    shell:
        'echo {output}'