
rule trinity:
    input:
        left=["reads/reads.left.fq.gz", "reads/reads2.left.fq.gz"],
        right=["reads/reads.right.fq.gz", "reads/reads2.right.fq.gz"]
    output:
        "trinity_out_dir/Trinity.fasta"
    log:
        'logs/trinity/trinity.log'
    params:
        options=""
    threads: 4
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_gb=10
    wrapper:
        "main/wrappers/trinity"
