GALAH

More scalable dereplication for metagenome assembled genomes

URL: https://github.com/wwood/galah

Example

This wrapper can be used in the following way:

rule galah_fas:
    input:
        fas=["fas/a.fa", "fas/b.fas.bz2", "fas/c.fasta.gz"],
    output:
        clusters="results.fas.tsv",
        repres="results.fas.list",
    log:
        "logs/out.fas.log",
    params:
        extra="--precluster-ani 0.9 --ani 0.95",
    threads: 2
    resources:
        mem_mb=50,
    wrapper:
        "v5.3.0-16-g710597c/bio/galah"


use rule galah_fas as galah_fas_list with:
    input:
        fas_list="fas/a.fas_list",
    output:
        clusters="results.fas_list.tsv",
        repres="results.fas_list.list",
    log:
        "logs/out.fas_list.log",

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

• galah=0.4.2

Input/Output

Input:

• FASTA files

Output:

• clusters: representative FASTA<TAB>member lines

• repres: paths to representative FAS files

Params

• extra: additional program arguments

Authors

• Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2023, Filipe G. Vieira"
__license__ = "MIT"

from snakemake.shell import shell


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


fas = snakemake.input.get("fas", "")
if fas:
    fas = f"--genome-fasta-files {' '.join(fas)}"


fas_list = snakemake.input.get("fas_list", "")
if fas_list:
    fas_list = f"--genome-fasta-list {fas_list}"


clusters = snakemake.output.get("clusters", "")
if clusters:
    clusters = f"--output-cluster-definition {clusters}"


repres = snakemake.output.get("repres", "")
if repres:
    repres = f"--output-representative-list {repres}"


shell(
    "galah cluster"
    " --threads {snakemake.threads}"
    " {fas}"
    " {fas_list}"
    " {extra}"
    " {clusters}"
    " {repres}"
    " {log}"
)