HISAT2 ALIGN

Map reads with hisat2.

URL: http://daehwankimlab.github.io/hisat2

Example

This wrapper can be used in the following way:

rule hisat2_align:
    input:
        reads=["reads/{sample}_R1.fastq", "reads/{sample}_R2.fastq"],
        idx="index/",
    output:
        "mapped/{sample}.bam",
    log:
        "logs/hisat2_align_{sample}.log",
    params:
        extra="",
    threads: 2
    wrapper:
        "v3.0.4/bio/hisat2/align"

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.

Notes

• The -S flag must not be used since output is already directly piped to samtools for compression.

• The –threads/-p flag must not be used since threads is set separately via the snakemake threads directive.

• The wrapper does not yet handle SRA input accessions.

• No reference index files checking is done since the actual number of files may differ depending on the reference sequence size. This is also why the index is supplied in the params directive instead of the input directive.

Software dependencies

• hisat2=2.2.1

• samtools=1.18

Input/Output

Input:

• reads: either 1 or 2 FASTQ files with reads

Output:

• bam file with mapped reads

Params

• idx: prefix of index file path (required)

• extra: additional parameters

Authors

• Wibowo Arindrarto

Code

__author__ = "Wibowo Arindrarto"
__copyright__ = "Copyright 2016, Wibowo Arindrarto"
__email__ = "bow@bow.web.id"
__license__ = "BSD"


import os
from pathlib import Path
from snakemake.shell import shell

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

# Input file wrangling
reads = snakemake.input.get("reads")
if isinstance(reads, str):
    input_flags = "-U {0}".format(reads)
elif len(reads) == 1:
    input_flags = "-U {0}".format(reads[0])
elif len(reads) == 2:
    input_flags = "-1 {0} -2 {1}".format(*reads)
else:
    raise RuntimeError(
        "Reads parameter must contain at least 1 and at most 2" " input files."
    )

ht2_files = Path(snakemake.input.idx).glob("*.ht2")
idx_prefix = os.path.commonprefix(list(ht2_files)).rstrip(".")

# Executed shell command
shell(
    "(hisat2 {extra} "
    "--threads {snakemake.threads} "
    " -x {idx_prefix} {input_flags} "
    " | samtools view -Sbh -o {snakemake.output[0]} -) "
    " {log}"
)