bioconda.wdl

# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2017

# Bioconda installs

task installPrefix {
    Array[String] requirements
    String prefix
    String? condaPath
    command {
        ${default="conda" condaPath} create \
        --json -q \
        --yes \
        --override-channels \
        --channel bioconda \
        --channel conda-forge \
        --channel defaults \
        --channel r \
        --prefix ${prefix} \
        ${sep=' ' requirements}
    }
    output {
        File condaEnvPath=prefix
    }
 }