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:
"v0.87.0/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
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}"
)