Add rule for TIN score calculation

See https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline/issues/4#note_15229 for links to tool and Docker image

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My scaffolding from the test workflow:

rule TIN_rule:
    input:
        TMP_output = os.path.join("{output_dir}", "dir_created"),
        SCRIPT = \
            os.path.join(config["src_dir"], "mz-TIN.transcript_wide.v2.py")
    output:
        TIN_TSV = \
            os.path.join("{output_dir}", "TIN_speeded_full.tsv")
    params:
        LOG_cluster_log = \
            os.path.join("{output_dir}", "cluster_log", \
                "TIN_rule.log"),
        queue = "1day",
        time = "23:00:00"
    log:
        LOG_local_log = \
            os.path.join("{output_dir}", "local_log", \
                "TIN_rule.log"),
    resources:
        threads = 8,
        mem = 32000
    benchmark:
        os.path.join("{output_dir}",
            "cluster_log", "TIN_rule_benchmark.log")
    conda:
        "packages.yaml"
    singularity:
        ""
    shell:
        """
        python {input.SCRIPT} \
        -i /scicore/home/zavolan/GROUP/SpeedUpTIN/sample_BAMs/GSM1862178.bam \
        -r /scicore/home/zavolan/GROUP/SpeedUpTIN/full_transcripts.protein_coding.bed \
        -c 0 \
        --names "sample_name" \
        -n 100 \
        1> {output.TIN_TSV} \
        2> {log.LOG_local_log};
        """

Thanks!

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changed title from Include rule for TIN score calculation to Add rule for TIN score calculation

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assigned to @bakma

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changed milestone to %v0.1.0 release

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mentioned in merge request !25 (merged)

Closed by !25 (merged)

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closed