Clash of names when using merqury trio mode (with hap-mers)

[Audald]

Hi there 👋🏽,

I realized that merqury generates unreliable results when the haplotype-resolved assemblies .fasta have the same name (albeit different paths). The .qv and completeness results seem to indicate that only one of the two files is used. This is the Snakemake rule I am running:

rule merqury:
    input:
        meryl_long = kmer_path + "genome.meryl", #long-read meryl database
        meryl_pat = kmer_path "pat.hapmer.meryl", #short-read parental database
        meryl_mat = kmer_path "mat.hapmer.meryl",  #short-read maternal database
        fasta_1 = out_path + "assembly_1/assembly.asm.dip.p_ctg.fasta", #haplotype-resolved assembly
        fasta_2 = out_path + "assembly_2/assembly.asm.dip.p_ctg.fasta" #haplotype-resolved assembly
    output:
        hist = out_path + "assembly/merqury_trio/genome.hist"
    params:
        path = out_path + "assembly/merqury_trio",
        out = "assembly"
    threads: 4
    resources:
        mem_mb = 1250,
        walltime = '3h'
    shell:
        '''
        cd {params.path} \n \
        merqury.sh {input.meryl_long} {input.meryl_mat} {input.meryl_pat} {input.fasta_1} {input.fasta_2} {params.out}
        '''

The results seem correct when different names are used (e.g. assembly.asm.dip.hap1.p_ctg.fasta and assembly.asm.dip.hap1.p_ctg.fasta) but I thought I'd share that. Thanks!