

rule all:
    input:
        "salmon_mapping/quant.sf",
        "salmon_mapping_pe/quant_pe.sf",



rule salmon_se_mapping:
    input:
        fastq="test_R1.fastq.gz",
        index="salmon_index/salmon.done"
    output:
        quant="salmon_mapping/quant.sf"
    params:
        options='-l A',
        genome_dir="salmon_index"
    threads: 1
    log:
        "salmon_mapping/salmon.log"
    wrapper:
        "main/wrappers/salmon/align"



rule salmon_mapping_pe:
    input:
        fastq=("test_R1.fastq.gz", "test_R2.fastq.gz"),
        index="salmon_index/salmon.done"
    output:
        # output named differently from default on purpose to test
        # the mv command
        quant="salmon_mapping_pe/quant_pe.sf"
    params:
        options='-l A',
        genome_dir="salmon_index"
    threads: 1
    log:
        "salmon_mapping_pe/salmon.log"
    wrapper:
        "main/wrappers/salmon/align"



