Description of feature

Dear nf-core & pangenome team,

I have a few questions about your great program.

Based on the link (https://github.com/nf-core/pangenome/blob/1.0.0/modules/nf-core/wfmash/main.nf), it appears that wfmash performs all-vs-all alignment on a single node.

wfmash \\
    ${fasta_gz} \\
    $query \\
    $query_list \\
    --threads $task.cpus \\
    $paf_mappings \\
    $args > ${prefix}.paf

From my trials, this is indeed the case.

I am trying to speed up the wfmash process on multiple nodes (PBSpro) by running parallel jobs. My idea is to perform one-vs-all alignments for each node from an input full genome dataset (120 human pangenomes), and then merge the results into a single paf file for further analysis.

1. Do you have any recommendations for tweaking the wfmash code to achieve this?
2. If I run one-vs-all alignments on each node, will the merged paf file be equivalent to an all-vs-all alignment? Theoretically, I assume the final outcome should be the same.

Looking forward to your insights.

Kind regards,

Taek