KALLISTO INDEX¶
Index a transcriptome using kallisto.
Example¶
This wrapper can be used in the following way:
rule kallisto_index:
input:
fasta = "{transcriptome}.fasta"
output:
index = "{transcriptome}.idx"
params:
extra = "--kmer-size=5"
log:
"logs/kallisto_index_{transcriptome}.log"
threads: 1
wrapper:
"0.71.0/bio/kallisto/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¶
kallisto==0.45.0
Authors¶
- Joël Simoneau
Code¶
"""Snakemake wrapper for Kallisto index"""
__author__ = "Joël Simoneau"
__copyright__ = "Copyright 2019, Joël Simoneau"
__email__ = "simoneaujoel@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
# Creating log
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")
# Allowing for multiple FASTA files
fasta = snakemake.input.get("fasta")
assert fasta is not None, "input-> a FASTA-file is required"
fasta = " ".join(fasta) if isinstance(fasta, list) else fasta
shell(
"kallisto index " # Tool
"{extra} " # Optional parameters
"--index={snakemake.output.index} " # Output file
"{fasta} " # Input FASTA files
"{log}" # Logging
)