Implement Salmon aligner about seq2science HOT 2 CLOSED

elif config['aligner'] == 'salmon':
    rule salmon_index:
        input:
            expand("{genome_dir}/{{assembly}}/{{assembly}}.fa", **config)
        output:
            directory(expand("{genome_dir}/{{assembly}}/index/{aligner}/", **config))
        log:
            expand("{log_dir}/{aligner}_index/{{assembly}}.log", **config)
        benchmark:
            expand("{benchmark_dir}/{aligner}_index/{{assembly}}.benchmark.txt", **config)[0]
        threads: 4
        conda:
            "../envs/salmon.yaml"
        shell:
            "salmon index -t {input} -i {output} --threads {threads} > {log} 2&1"


    rule salmon_quant:
        input:
            reads=get_reads,
            index=expand("{genome_dir}/{{assembly}}/index/{aligner}/", **config)
        output:
            pipe(expand("{result_dir}/{aligner}/{{sample}}-{{assembly}}.bampipe", **config))
        log:
            expand("{log_dir}/{aligner}_align/{{sample}}-{{assembly}}.log", **config)
        benchmark:
            expand("{benchmark_dir}/{aligner}_align/{{sample}}-{{assembly}}.benchmark.txt", **config)[0]
        params:
            input=lambda wildcards, input: f'-r {input.reads}' if config['layout'][wildcards.sample] == 'SINGLE' else \
                                           f'-1 {input.reads[0]} -2 {input.reads[1]}'
        threads: 20
        conda:
            "../envs/salmon.yaml"
        shell:
            """
            salmon quant -i {input.index} {params.input} 1> {output} 2> {log}
            """