HISAT2 INDEX

Create index with hisat2.

Example

This wrapper can be used in the following way:

rule hisat2_index:
    input:
        fasta = "{genome}.fasta"
    output:
        directory("index_{genome}")
    params:
        prefix = "index_{genome}/"
    log:
        "logs/hisat2_index_{genome}.log"
    threads: 2
    wrapper:
        "v2.6.0/bio/hisat2/index"

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

• hisat2=2.2.1
• samtools=1.17

Input/Output

Input:

• sequence: list of FASTA files of list of sequences

Output:

• Directory of the hisat2 custom index.

Params

• prefix: prefix of index file path (required). Must be related to output
• extra: additional parameters

Authors

• Joël Simoneau

Code

"""Snakemake wrapper for HISAT2 index"""

__author__ = "Joël Simoneau"
__copyright__ = "Copyright 2019, Joël Simoneau"
__email__ = "simoneaujoel@gmail.com"
__license__ = "MIT"

import os
from snakemake.shell import shell

# Creating log
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")

# Allowing for multiple FASTA files
fasta = snakemake.input.get("fasta")
assert fasta is not None, "input-> a FASTA-file or a sequence is required"
input_seq = ""
if not "." in fasta:
    input_seq += "-c "
input_seq += ",".join(fasta) if isinstance(fasta, list) else fasta

hisat_dir = snakemake.params.get("prefix", "")
if hisat_dir:
    os.makedirs(hisat_dir)

shell(
    "hisat2-build {extra} "
    "-p {snakemake.threads} "
    "{input_seq} "
    "{snakemake.params.prefix} "
    "{log}"
)