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<p>我试图将名为samples的<code>--config</code>参数传递给snakemake函数。似乎不管我怎么传递,所有的下划线都被删除了?有什么建议吗,还是我做错了什么</p>
<p><code>snakemake -s snakefile.py all --configfile /share/biocore/keith/dennislab/snakemake/templates/tagseq.json --config samples=60_3_6,</code></p>
<p><strong>或</strong></p>
<p><code>snakemake -s snakefile.py all --configfile /share/biocore/keith/dennislab/snakemake/templates/tagseq.json --config samples="60_3_6"</code></p>
<p><strong>或</strong></p>
<p><code>snakemake -s snakefile.py all --configfile /share/biocore/keith/dennislab/snakemake/templates/tagseq.json --config samples='60_3_6'</code></p>
<hr/>
<p>所有这些都会为snakefile中的配置字典生成这样的结果(注意最后的samples参数)</p>
<p><code>{'__default__': OrderedDict([('__comment1', 'running_locally=[True,False] ~ type=[PE,SE,tagseq]'), ('running_locally', 'False'), ('type', 'tagseq'), ('__comment2', 'Path to the file containing a column of sample names'), ('samples_file', '/share/biocore/keith/dennislab/rhesus_tagseq/samples.txt')]), 'project': OrderedDict([('basename', '/share/biocore/keith/dennislab'), ('id', 'PE'), ('fastqs', 'rhesus_tagseq'), ('human_rrna_ref', '/share/biocore/keith/workshop/rnaseq_examples/References/human_rrna.fasta'), ('star_ref', '/share/biocore/keith/dennislab/star.overlap100.gencode')]), 'hts_star': OrderedDict([('__comment', 'This is for running one sample for htspreproc > star'), ('job-name', 'hts_star_'), ('n', 1), ('ntasks', 9), ('partition', 'production'), ('time', '120'), ('mem', '32000'), ('__comment2', 'The name of the sample and analysis type will be inserted before .out and .err'), ('output', 'slurm_out/hts_star_.out'), ('error', 'slurm_out/hts_star_.err'), ('mail-type', 'NONE'), ('mail-user', 'kgmitchell@ucdavis.edu')]), 'samples': (6036,)}</code></p>