SEQTK-SEQ¶
Common transformations of FASTA/Q using seqtk
URL: https://github.com/lh3/seqtk
Example¶
This wrapper can be used in the following way:
rule seqtk_seq_fastq_to_fasta:
input:
"{prefix}.fastq",
output:
"{prefix}.fasta",
log:
"{prefix}.log",
params:
extra="-A",
wrapper:
"v1.19.1/bio/seqtk/seq"
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¶
seqtk=1.3
Authors¶
- William Rowell
Code¶
"""Snakemake wrapper seqtk seq subcommand"""
__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("(seqtk seq {extra} {snakemake.input} > {snakemake.output}) {log}")