SALMON_INDEX

Index a transcriptome assembly with salmon

URL:

Example

This wrapper can be used in the following way:

rule salmon_index:
    input:
        "assembly/transcriptome.fasta"
    output:
        directory("salmon/transcriptome_index")
    log:
        "logs/salmon/transcriptome_index.log"
    threads: 2
    params:
        # optional parameters
        extra=""
    wrapper:
        "v1.1.0/bio/salmon/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

• salmon==0.14.1

Input/Output

Input:

• assembly fasta

Output:

• indexed assembly

Authors

• Tessa Pierce

Code

"""Snakemake wrapper for Salmon Index."""

__author__ = "Tessa Pierce"
__copyright__ = "Copyright 2018, Tessa Pierce"
__email__ = "ntpierce@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")

shell(
    "salmon index -t {snakemake.input} -i {snakemake.output} "
    " --threads {snakemake.threads} {extra} {log}"
)