
rule all:
    input: 
        "star_index/star.done",
        "star_index2/star.done",
        "star_index3/star.done"


rule star_index:
    input:
        fasta="genome.fasta"
    output:
        done = "star_index/star.done"
    params:
        # no options and no wkdir set on purpose for testing
    threads: 2
    log:
        "star_index/star.log"
    wrapper:
        "main/wrappers/star/index"


rule star_index2:
    input:
        fasta="genome.fasta",
        annotation="genome.gtf"
    output:
        done = "star_index2/star.done"
    params:
        options= " ",
        wkdir="star_index2"
    threads: 2
    log:
        "star_index2/star.log"
    wrapper:
        "main/wrappers/star/index"


rule star_index3:
    input:
        fasta="genome.fasta",
        annotation="genome.gff3"
    output:
        done = "star_index3/star.done"
    params:
        # set sjdbOverhang specifically for testing
        wkdir="star_index3",
        sjdbOverhang=150,
        exonParentTranscript= 'Parent'
    threads: 2
    log:
        "star_index3/star.log"
    wrapper:
        "main/wrappers/star/index"
