snakemake学习笔记003：stringtie合并转录本

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wx6221d9080e88d 2022-07-16 00:26:47 ©著作权

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SRR, = glob_wildcards("output.gtf/"+"{srr}.gtf")
#SRR = ["ERR188401","ERR204916"]
#rule all:
#    input:
#        expand("output.gtf/"+"{srr}.gtf",srr=SRR),

rule gtflist:
    input:
        gtffiles = expand("output.gtf/"+"{srr}.gtf",srr=SRR)
    output:
        output_txt = "MergedList.txt"
    run:
        with open(output.output_txt,'w') as f:
            for gtf in input.gtffiles:
                print(gtf,file=f)

第一行SRR后面有一个逗号

最开始没写这个逗号，一直遇到报错

snakemake学习笔记003：stringtie合并转录本_java

image.png

Building DAG of jobs... MissingInputException in line 3 of /mnt/shared/scratch/myan/private/practice_data/RNAseq/snakemake.rnaseq/gtf_list.py: Missing input files for rule all: output.gtf/['ERR188337', 'ERR188245', 'ERR188428', 'ERR188401', 'ERR204916', 'ERR188383', 'ERR188104', 'ERR188257', 'ERR188273', 'ERR188044', 'ERR188234', 'ERR188454'].gtf