FATOTWOBIT

Convert *.fa file to *.2bit file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)

Example

This meta-wrapper can be used in the following way:

# Example: from *.fa file
rule faToTwoBit_fa:
    input:
        "{sample}.fa"
    output:
        "{sample}.2bit"
    log:
        "logs/{sample}.fa_to_2bit.log"
    params:
        "" # optional params string
    wrapper:
        "0.66.0/bio/ucsc/faToTwoBit"

# Example: from *.fa.gz file
rule faToTwoBit_fa_gz:
    input:
        "{sample}.fa.gz"
    output:
        "{sample}.2bit"
    log:
        "logs/{sample}.fa-gz_to_2bit.log"
    params:
        "" # optional params string
    wrapper:
        "0.66.0/bio/ucsc/faToTwoBit"

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

  • Roman Cherniatchik

Code