snakemake shell脚本中的输入组合

Question

我有以下bash脚本，我想将其转换为蛇文件：

mmseqs rbh flye_db megahit_db flye_megahit_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
mmseqs rbh flye_db metaspades_db flye_metaspades_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
mmseqs rbh megahit_db metaspades_db megahit_metaspades_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12

我设法提出以下内容，但想知道是否存在使用正则表达式或扩展来进一步改善代码的方法：

rule mmseq2_compare:
    input:
        mm1=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="flye"),
        mm2=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="megahit"),
        mm3=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="metaspades_hybrid")
    output: 
        mo1=os.path.join(RESULTS_DIR, "annotation/mmseq2/flye_megahit_rbh"),
        mo2=os.path.join(RESULTS_DIR, "annotation/mmseq2/flye_metaspades_hybrid_rbh"),
        mo3=os.path.join(RESULTS_DIR, "annotation/mmseq2/megahit_metaspades_hybrid_rbh")
    log: os.path.join(RESULTS_DIR, "annotation/mmseq2/compare.mmseq2.log")
    conda: "cd-hit.yml"
    shell:
        """
        (date &&\
        mmseqs rbh {input.mm1} {input.mm2} {output.mo1} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
        mmseqs rbh {input.mm1} {input.mm3} {output.mo2} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
        mmseqs rbh {input.mm2} {input.mm3} {output.mo3} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
        date) &> >(tee {log})
        """

使用3个汇编程序（flye，megahit和metaspades_hybrid），有什么方法可以消除冗余，尤其是在'shell'中？

谢谢！

空运行输出

Building DAG of jobs...
Job counts:
        count   jobs
        1       all
        1       mmseq_compare
        2

[Thu Mar 26 12:25:14 2020]
rule mmseq_compare:
    input: results/annotation/mmseq2/flye_db, results/annotation/mmseq2/megahit_db
    output: results/annotation/mmseq2/flye_megahit_rbh
    jobid: 1
    wildcards: assembler1=flye, assembler2=megahit

mmseqs rbh results/annotation/mmseq2/flye_db results/annotation/mmseq2/megahit_db results/annotation/mmseq2/flye_megahit_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12

[Thu Mar 26 12:25:14 2020]
localrule all:
    input: results/annotation/mmseq2/flye_megahit_rbh, results/annotation/mmseq2/flye_metaspades_hybrid_rbh, results/annotation/mmseq2/megahit_metaspades_hybrid_rbh
    jobid: 0

Job counts:
        count   jobs
        1       all
        1       mmseq_compare
        2
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.```

Answer 1