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veg / flea-pipeline

A pipeline for long-read sequencing data.
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Request for a test case and clarification on reference and DB paths #89

Open jong3 opened 1 month ago

jong3 commented 1 month ago

Hello,

Thank you for developing the FLEA tool. I’m currently trying to set up the workflow, but I’ve encountered a couple of issues:

  1. Both websites mentioned in the paper https://doi.org/10.1371/journal.pcbi.1006498: http://flea.datamonkey.org/ http://flea.murrell.group/view/P018 appear to be inaccessible. Could you please provide a test case that I can use to ensure the tool is working properly?

  2. Regarding the paths mentioned in the nextflow.config file, specifically:

    params.reference_dir = "/path/to/references"
params.reference_dna = "${params.reference_dir}/HXB2_env.fasta"
params.reference_protein = "${params.reference_dir}/HXB2_env.translated.fasta"
params.reference_coordinates = "${params.reference_dir}/HXB2_env.coordinates.txt"
params.reference_db = "${params.reference_dir}/LANLsubtypeRef.fasta"
params.contaminants_db = "${params.reference_dir}/ContaminantRef.fasta"

    Could you provide a reference test case, or guide us on how to prepare these reference and DB files? Any example paths or downloadable references would be extremely helpful for getting started.

Thank you for your assistance!

Best regards,