SOURMASH_COMPUTE¶
Build a MinHash signature for a transcriptome, genome, or reads
Example¶
This wrapper can be used in the following way:
rule sourmash_reads:
input:
"reads/a.fastq"
output:
"reads.sig"
log:
"logs/sourmash/sourmash_compute_reads.log"
threads: 2
params:
# optional parameters
k = "31",
scaled = "1000",
extra = ""
wrapper:
"v1.12.2/bio/sourmash/compute"
rule sourmash_transcriptome:
input:
"assembly/transcriptome.fasta"
output:
"transcriptome.sig"
log:
"logs/sourmash/sourmash_compute_transcriptome.log"
threads: 2
params:
# optional parameters
k = "31",
scaled = "1000",
extra = ""
wrapper:
"v1.12.2/bio/sourmash/compute"
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¶
sourmash==2.0.0a7
Authors¶
- Lisa K. Johnson
Code¶
"""Snakemake wrapper for sourmash compute."""
__author__ = "Lisa K. Johnson"
__copyright__ = "Copyright 2018, Lisa K. Johnson"
__email__ = "ljcohen@ucdavis.edu"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
scaled = snakemake.params.get("scaled", "1000")
k = snakemake.params.get("k", "31")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"sourmash compute --scaled {scaled} -k {k} {snakemake.input} -o {snakemake.output}"
" {extra} {log}"
)