DIAMOND BLASTX

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

URL: https://github.com/bbuchfink/diamond/wiki

Example

This wrapper can be used in the following way:

rule diamond_blastx:
    input:
        fname_fastq = "{sample}.fastq",
        fname_db = "db.dmnd"
    output:
        fname = "{sample}.tsv.gz"
    log:
        "logs/diamond_blastx/{sample}.log"
    params:
        extra="--header --compress 1"
    threads: 8
    wrapper:
        "v3.8.0-1-g149ef14/bio/diamond/blastx"

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

• diamond=2.1.9

Input/Output

Input:

• fname_fastq: Fastq query file

• fname_db: Path to diamon database

Output:

• fname: Path to query result

Params

• extra: Optional parameters besides –threads, –db, –query, and –out.

Authors

• Kim Philipp Jablonski

Code

__author__ = "Kim Philipp Jablonski"
__copyright__ = "Copyright 2020, Kim Philipp Jablonski"
__email__ = "kim.philipp.jablonski@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell


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


shell(
    "diamond blastx"
    " --threads {snakemake.threads}"
    " --db {snakemake.input.fname_db}"
    " --query {snakemake.input.fname_fastq}"
    " --out {snakemake.output.fname}"
    " {extra}"
    " {log}"
)