PANDORA INDEX
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:
"v5.0.0/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 filekmer_prgs
: A directory of the index kmer PRGs in GFA format
Params
options
: Any options other than threads (see docs)
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}")