我认为我有一个简单的问题,但我不知道如何解决。
我的输入文件夹包含以下文件:
AAAAA_S1_R1_001.fastq
AAAAA_S1_R2_001.fastq
BBBBB_S2_R1_001.fastq
BBBBB_S2_R2_001.fastq
我的snakemake代码:
import glob
samples = [os.path.basename(x) for x in sorted(glob.glob("input/*.fastq"))]
name = []
for x in samples:
if "_R1_" in x:
name.append(x.split("_R1_")[0])
NAME = name
rule all:
input:
expand("output/{sp}_mapped.bam",sp=NAME),rule bwa:
input:
R1 = "input/{sample}_R1_001.fastq",R2 = "input/{sample}_R2_001.fastq"
output:
mapped = "output/{sample}_mapped.bam"
params:
ref = "refs/AF086833.fa"
run:
shell("bwa mem {params.ref} {input.R1} {input.R2} | samtools sort > {output.mapped}")
输出文件名为:
AAAAA_S1_mapped.bam
BBBBB_S2_mapped.bam
我希望输出文件为:
AAAAA_mapped.bam
BBBBB_mapped.bam
如何在bwa规则之前或之后更改输出名称或重命名文件。