include: 'common.snakemake'

def get_all_inputs(wildcards):

    inputs = []

    if config['paired_end']:

        inputs += expand('{output_dir}/unmapped/{sample_id}/clean_{mate_index}.fastq.gz',

            output_dir=output_dir, sample_id=sample_ids, mate_index=[1, 2])

    else:

        inputs += expand('{output_dir}/unmapped/{sample_id}/clean.fastq.gz',

            output_dir=output_dir, sample_id=sample_ids, mate_index=[1, 2])

    return inputs

rule all:

    input:

        get_all_inputs

rule rename_fastq_pe:

    input:

        auto_gzip_input('{output_dir}/cutadapt/{sample_id}_{mate_index}.fastq')

    output:

        '{output_dir}/unmapped/{sample_id}/clean_{mate_index}.fastq.gz'

    threads: 

        1

    wildcard_constraints:

        mate_index='[12]'

    shell:

        r'''{bin_dir}/auto_uncompress {input} \

            | awk 'NR%4==1{{printf "@%012d\n", int(NR/4);next}} NR%4==3{{printf "+\n";next}} {{print}}' \

            | pigz -c -p {threads} > {output}

        '''

rule rename_fastq_se:

    input:

        auto_gzip_input('{output_dir}/cutadapt/{sample_id}.fastq')

    output:

        '{output_dir}/unmapped/{sample_id}/clean.fastq.gz'

    threads: 

        1

    shell:

        r'''{bin_dir}/auto_uncompress {input} \

            | awk 'NR%4==1{{printf "@%012d\n", int(NR/4);next}} NR%4==3{{printf "+\n";next}} {{print}}' \

            | pigz -c -p {threads} > {output}

        '''