PANDORA INDEX

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Index population reference graph (PRG) sequences.

URL: https://github.com/rmcolq/pandora/wiki/Usage#build-index

Example

This wrapper can be used in the following way:

rule pandora_index:
    input:
        "{gene}/prg.fa",
    output:
        index="{gene}/prg.fa.k15.w14.idx",
        kmer_prgs=directory("{gene}/kmer_prgs"),
    log:
        "pandora_index/{gene}.log",
    params:
        options="-v -k 15 -w 14",
    threads: 1
    wrapper:
        "v3.10.2-32-gf4e5b66/bio/pandora/index"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

  • pandora=0.9.2

Input/Output

Input:

  • A PRG file (made by make_prg <https://github.com/iqbal-lab-org/make_prg>) to index

Output:

  • index: A pandora index file

  • kmer_prgs: A directory of the index kmer PRGs in GFA format

Params

  • options: Any options other than threads (see docs)

Authors

  • Michael Hall

Code

"""Snakemake wrapper for indexing population reference graph (PRG) sequences with
pandora
"""

__author__ = "Michael Hall"
__copyright__ = "Copyright 2021, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=False)
options = snakemake.params.get("options", "")

shell("pandora index -t {snakemake.threads} {options} {snakemake.input} {log}")