74 lines (70 with data), 3.0 kB

include: '{{ common_snakemake }}'

rule all:
    input:
        unmapped=expand('{output_dir}/unmapped/{sample_id}/other.fa.gz',
            output_dir=output_dir, sample_id=sample_ids),
        bam=expand('{output_dir}/gbam/{sample_id}/other.bam',
            output_dir=output_dir, sample_id=sample_ids),
        {% for rna_type in rna_types %}
        {% if loop.last %}
        tbam_{{ rna_type }}=expand('{output_dir}/tbam/{sample_id}/{{ rna_type }}.bam',
            output_dir=output_dir, sample_id=sample_ids)
        {% else %}
        tbam_{{ rna_type }}=expand('{output_dir}/tbam/{sample_id}/{{ rna_type }}.bam',
            output_dir=output_dir, sample_id=sample_ids),
        {% endif %}
        {% endfor %}

{% 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=config['genome_dir'] + '/index/{{ aligner }}/{{ rna_type }}.1.bt2'
        {% elif rna_type == 'spikein' %}
        index=config['spikein_dir'] + '/index/{{ aligner }}/{{ rna_type }}.1.bt2'
        {% else %}
        index=config['genome_dir'] + '/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=config['genome_dir'] + '/index/{{ aligner }}/{{ rna_type }}'
        {% elif rna_type == 'spikein' %}
        index=config['spikein_dir'] + '/index/{{ aligner }}/{{ rna_type }}'
        {% else %}
        index=config['genome_dir'] + '/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=config['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=config['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}
        '''