PICARD CREATESEQUENCEDICTIONARY

Create a .dict file for a given FASTA file

Example

This wrapper can be used in the following way:

rule create_dict:
    input:
        "genome.fasta"
    output:
        "genome.dict"
    log:
        "logs/picard/create_dict.log"
    params:
        extra=""  # optional: extra arguments for picard.
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024
    wrapper:
        "0.73.0/bio/picard/createsequencedictionary"

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

• picard==2.22.1
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• FASTA file

Output:

• .dict file

Authors

• Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


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

shell(
    "picard "
    "CreateSequenceDictionary "
    "{java_opts} {extra} "
    "R={snakemake.input[0]} "
    "O={snakemake.output[0]} "
    "{log}"
)