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Description
openedon Aug 1, 2024
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.
- Do you have any recommendations for tweaking the wfmash code to achieve this?
- 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
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