PICARD CREATESEQUENCEDICTIONARY

Create a .dict file for a given FASTA file

Software dependencies

  • picard ==2.22.1

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.
    wrapper:
        "0.67.0/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.

Authors

  • Johannes Köster

Code

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


from snakemake.shell import shell


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

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