single_end.snakefile.smk

current_rule = 'remove_adapters_cutadapt'
rule remove_adapters_cutadapt:
    '''
        Remove adapters
    '''
    input:
        reads = os.path.join(
            config["output_dir"],
            "samples",
            "{sample}",
            "start",
            "{sample}.fq1.fastq.gz")

    output:
        reads = temp(os.path.join(
            config["output_dir"],
            "samples",
            "{sample}",
            "{sample}.se.remove_adapters_mate1.fastq.gz"))

    params:
        adapters_3 = lambda wildcards:
            get_sample(
                'fq1_3p',
                search_id='index',
                search_value=wildcards.sample),
        adapters_5 = lambda wildcards:
            get_sample(
                'fq1_5p',
                search_id='index',
                search_value=wildcards.sample),
        additional_params = parse_rule_config(
            rule_config,
            current_rule=current_rule,
            immutable=(
                '-a',
                '-A',
                '-g',
                '-G',
                '-o',
                '-p',
                )
            )

    singularity:
        "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"

    conda:
        os.path.join(workflow.basedir, "envs", "cutadapt.yaml")

    threads: 8

    log:
        stderr = os.path.join(
            config["log_dir"],
            "samples",
            "{sample}",
            current_rule + ".se.stderr.log"),
        stdout = os.path.join(
            config["log_dir"],
            "samples",
            "{sample}",
            current_rule + ".se.stdout.log")
    shell:
        "(cutadapt \
        -j {threads} \
        -a {params.adapters_3} \
        -g {params.adapters_5} \
        -m 1 \
        {params.additional_params} \