BWA ALN¶
Map reads with bwa aln. For more information about BWA see BWA documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule bwa_aln:
input:
"reads/{sample}.{pair}.fastq"
output:
"sai/{sample}.{pair}.sai"
params:
index="genome",
extra=""
log:
"logs/bwa_aln/{sample}.{pair}.log"
threads: 8
wrapper:
"0.80.1/bio/bwa/aln"
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¶
bwa==0.7.17
Authors¶
- Julian de Ruiter
Code¶
"""Snakemake wrapper for bwa aln."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"bwa aln"
" {extra}"
" -t {snakemake.threads}"
" {snakemake.params.index}"
" {snakemake.input[0]}"
" > {snakemake.output[0]} {log}"
)