如何在snakemake规则中使用bash for循环_Bash_Snakemake

如何在snakemake规则中使用bash for循环

bash

如何在snakemake规则中使用bash for循环,bash,snakemake,Bash,Snakemake,我很抱歉，如果这似乎类似于其他帖子，但我是一个新手，而且我正在尝试将我的bashfor循环，它将一个串联文件（*.fastq.gz）拆分为单独的片段（*.fastq）并转换为蛇形规则。我的蛇怪不断地抛出错误 Building DAG of jobs...MissingRuleException:No rule to produce 2 (if you use input functions make sure that they don't raise unexpected exception

我很抱歉，如果这似乎类似于其他帖子，但我是一个新手，而且我正在尝试将我的bash

for循环

，它将一个串联文件（

*.fastq.gz

）拆分为单独的片段（

*.fastq

）并转换为

蛇形规则

。我的蛇怪不断地抛出错误

Building DAG of jobs...MissingRuleException:No rule to produce 2 (if you use input functions make sure that they don't raise unexpected exceptions).

请参阅我的snakemake（

解复用\u fastq.smk

）脚本

我希望得到多个文件作为输出（但我事先不知道每个输入文件中有多少个碎片）

谢谢你的帮助

$ cat demultiplex_fastq.smk

configfile: "config/input_paths_fastq.yaml"

rule all:
    input:
        expand("results/{samples}/{samples}.fastq", samples=config["samples"])

rule demultiplex_fastq:
    input:
        fastq1=lambda wildcards: config["samples"][wildcards.samples]
    output:
         fastq_gz="results/{samples}/{samples}.fastq"
    log:
        "logs/demultiplex_fastq/{samples}_demultiplexed_fastq.txt"
    shell:
    """
    zcat {input.fastq1} |
    awk -v sname="{wildcards.samples}" '
        BEGIN {{FS = ":"}} 
        {{
            lane=${{4}};
            fileName = sname".lane."lane".fastq" 
            print > fileName
            for (i = 1; i <= 3; i++) {{
                getline
                print > fileName
            }}
        }}' 2> {log}
    """

$ cat input_paths_fastq.yaml

samples:
    SC173863_ACCTCCAA_L008_R2_001_HQ_paired: /Tumor/test_pipelines/SC173863_ACCTCCAA_L008_R2_001_HQ_paired.fastq.gz
    SC173866_CTGGCATA_L004_R1_001_HQ_paired: /Tumor/test_pipelines/SC173866_CTGGCATA_L004_R1_001_HQ_paired.fastq.gz

SC173863_ACCTCCAA_L008_R2_001_HQ_paired.lane1.fastq
SC173863_ACCTCCAA_L008_R2_001_HQ_paired.lane2.fastq
SC173863_ACCTCCAA_L008_R2_001_HQ_paired.lane3.fastq
SC173866_CTGGCATA_L004_R1_001_HQ_paired.lane1.fastq
SC173866_CTGGCATA_L004_R1_001_HQ_paired.lane2.fastq
SC173866_CTGGCATA_L004_R1_001_HQ_paired.lane3.fastq