Add rule to run salmon in PE mode

Add rule to run salmon in PE mode

################################################################################
### Salmon quantify based on reads
################################################################################

rule salmon_quant_reads_PE:
    input:
        mate_1_reads = os.path.join(config["output_dir"], "{sample}", "cutadapt", "trim_3p_adapter_mate1.fastq.gz"),
        mate_2_reads = os.path.join(config["output_dir"], "{sample}", "cutadapt", "trim_3p_adapter_mate2.fastq.gz"),
        index = os.path.join(config["output_dir"], "annotation", "annotation.filtered.salmon.idx"),
        transcriptid2geneid = os.path.join(config["output_dir"], "annotation", "annotation.filtered.transcriptid2geneid.txt")
    output:
        salmon_out = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads", "quant.sf"),
        salmon_genes_out = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads", "quant.genes.sf"),
    params:
        libType = "A",
        salmon_dir = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads")
    log:
        os.path.join(config["local_log"], "salmon_quant_reads_PE_{sample}.log")
    threads:    12
    conda:
        "envs/salmon.yaml"
    shell:
        "(salmon quant \
        --libType {params.libType} \
        --seqBias \
        --validateMappings \
        --threads {threads} \
        --writeUnmappedNames \
        --index {input.index} \
        --geneMap {input.transcriptid2geneid} \
        -1 {input.mate_1_reads} \
        -2 {input.mate_2_reads} \
        -o {params.salmon_dir}) &> {log}"

added Doing label

assigned to @katsanto

mentioned in merge request !4 (merged)

mentioned in commit 9017c055

closed via merge request !4 (merged)

removed Doing label

added 1 deleted label

mentioned in issue #48 (closed)

mentioned in merge request !15 (merged)

mentioned in commit ca9a2bb4

mentioned in commit 81f80f7a