include: 'common.snakemake'

def get_all_inputs(wildcards):

    inputs = []

    if config['paired_end']:

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

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

    else:

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

            output_dir=output_dir, sample_id=sample_ids)

    return inputs

rule all:

    input:

        get_all_inputs

rule fastq_to_fasta_pe:

    input:

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

    output:

        '{output_dir}/unmapped/{sample_id}/clean_{pair_index}.fa.gz'

    threads:

        config['threads_compress']

    wildcard_constraints:

        pair_index='[12]'

    shell:

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

            | fastq_to_fasta -r -n \

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

        '''

rule fastq_to_fasta_se:

    input:

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

    output:

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

    threads:

        config['threads_compress']

    shell:

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

            | fastq_to_fasta -r -n \

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

        '''