问题描述
我正在尝试使用 Snakemake 规则来拆分和处理大 bam 文件。在 splitBam 规则中,我将 Bam 拆分为我尝试在 Count 规则中使用的动态输出中。当我尝试这些时,我收到错误:
data/raw_data/set1/__snakemake_dynamic___R1.fq.gz
有什么办法可以迭代输入列表吗?谢谢!
rule SplitBam :
input:
sort = intermediate_path + "/bamSortByName/{sample}.sortByName.bam"
output:
sub = dynamic(intermediate_path +"/bamSortByName/{sample}.sortByName.REF_chr{part}.bam")
conda:
"env.yaml"
shell:
'bamtools split -in {input.sort} -reference'
rule TEcount :
input:
sub = intermediate_path +"/bamSortByName/{sample}.sortByName.REF_chr{part}.bam",annotation = config["ANNOTATION"],anno_te = config["GTFTE"]
output:
countT = final_path +"/repeats" +"/countTables/{sample}_{part}_TE_count.tsv"
conda:
"env.yaml"
params:
mp = main_path,sm = "{sample}"+"_"+"{part}",tablet = main_path + "{sample}_{part}_TE_count.tsv"
shell:
"python {params.mp}scripts/TEcount.py --format BAM --mode multi -b {input.sub} --GTF {input.annotation} --TE {input.anno_te} --stranded {strand} --project {params.sm} && mv -f {params.tablet} {output.countT}"
rule merge:
input:
splittable = dynamic( final_path +"/repeats" +"/countTables/{sample}_{part}_TE_count.tsv")
output:
mergetable = final_path + "/repeats" +"/countTables/{sample}_mergeTE_count.tsv"
params:
prefix= final_path + "/repeats"+"/countTables/{sample}_",sufix = "_TE_count.tsv"
shell:
"cat {params.prefix}*{params.sufix} > {output.mergetable}"
解决方法
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