{% for rna_type in rna_types %}

rule map_{{ rna_type }}:

    input:

        {% if loop.index0 == 0 %}

        reads='{output_dir}/unmapped/{sample_id}/clean.fa.gz',

        {% else %}

        reads='{output_dir}/unmapped/{sample_id}/{{ rna_types[loop.index0 - 1] }}.fa.gz',

        {% endif %}

        {% if rna_type in ['univec', 'rRNA', 'miRNA', 'circRNA'] %}

        index=genome_dir + '/index/{{ aligner }}/{{ rna_type }}.1.bt2'

        {% elif rna_type == 'spikein' %}

        index=config['spikein_dir'] + '/index/{{ aligner }}/{{ rna_type }}.1.bt2'

        {% else %}

        index=genome_dir + '/rsem_index/{{ aligner }}/{{ rna_type }}.1.bt2'

        {% endif %}

    output:

        unmapped='{output_dir}/unmapped/{sample_id}/{{ rna_type }}.fa.gz',

        bam='{output_dir}/tbam/{sample_id}/{{ rna_type }}.bam'

    params:

        {% if rna_type in ['univec', 'rRNA', 'miRNA', 'circRNA'] %}

        index=genome_dir + '/index/{{ aligner }}/{{ rna_type }}'

        {% elif rna_type == 'spikein' %}

        index=config['spikein_dir'] + '/index/{{ aligner }}/{{ rna_type }}'

        {% else %}

        index=genome_dir + '/rsem_index/{{ aligner }}/{{ rna_type }}'

        {% endif %}

    threads: 

        config['threads_mapping']

    shell:

        '''pigz -d -c {input.reads} \

        | bowtie2 -f -p {threads} --norc --sensitive --no-unal \

            --un-gz {output.unmapped} -x {params.index} - -S - \

        | samtools view -b -o {output.bam}

        '''

{% endfor %}

rule map_other:

    input:

        {% if (rna_types|length) == 0 %}

        reads='{output_dir}/unmapped/{sample_id}/clean.fa.gz',

        {% else %}

        reads='{output_dir}/unmapped/{sample_id}/{{ rna_types[-1] }}.fa.gz',

        {% endif %}

        index=genome_dir + '/genome_index/{{ aligner }}/genome.1.bt2'

    output:

        unmapped='{output_dir}/unmapped/{sample_id}/other.fa.gz',

        bam='{output_dir}/gbam/{sample_id}/other.bam'

    params:

        index=genome_dir + '/genome_index/{{ aligner }}/genome'

    shell:

        '''pigz -d -c {input.reads} \

        | bowtie2 -f -p {threads} --sensitive --no-unal \

            --un-gz {output.unmapped} -x {params.index} - -S - \

        | samtools view -b -o {output.bam}

        '''