Snakemake: HISAT2 alignment of many RNAseq reads against many genomes

问题

I have several genome files, all with suffix .1.ht2l to .8.ht2l

bob.1.ht2l
bob.2.ht2l
bob.3.ht2l
bob.4.ht2l 
bob.5.ht2l
bob.6.ht2l
bob.7.ht2l
bob.8.ht2l
steve.1.ht2l ....steve.8.ht2l and so on

and sereval RNAseq samples, like

flower_kevin_1.fastq.gz
flower_kevin_2.fastq.gz
flower_daniel_1.fastq.gz
flower_daniel_2.fastq.gz and so on also with different tissues.

I would like to align all rnaseq reds against the genomes. UPDATED:

workdir: "/path/to/aligned"  
(HISAT2_INDEX_PREFIX,)=glob_wildcards("/path/to/index/{prefix}.1.ht2l")
(SAMPLES,)=glob_wildcards("/path/to/{sample}_1.fastq.gz") 
print(HISAT2_INDEX_PREFIX)  
print (SAMPLES)

rule all:
    input: 
        expand("{prefix}.{sample}.bam", zip, prefix=HISAT2_INDEX_PREFIX, sample=SAMPLES)

rule hisat2:
    input:
        hisat2_index=expand("%s.{ix}.ht2l" % "/path/to/index/{prefix}", ix=range(1, 9)),
        fastq1="/path/to/{sample}_1.fastq.gz",
        fastq2="/path/to/{sample}_2.fastq.gz"
    output:
        bam = "{prefix}.{sample}.bam",
        txt = "{prefix}.{sample}.txt",
    log: "{prefix}.{sample}.snakemake_log.txt"
    threads: 5
    shell:
      "/Tools/hisat2-2.1.0/hisat2 -p {threads} -x {HISAT2_INDEX_PREFIX}"
      " -1 {input.fastq1} -2 {input.fastq2}  --summary-file {output.txt} |"
      "/Tools/samtools-1.9/samtools sort -@ {threads} -o {output.bam}"

I get missing input files error, I am sure the error is somewhere with suffixes, however,I do not know how to solve and any suggestion is much appreciated. UPDATE: ALL genome files bob.1.ht2l..bob.8.ht2l, steve.1.ht2l..steve.8.ht2l get invoked all at once, why is that?

回答1:

Let's compare these 2 lines:

(HISAT2_INDEX_PREFIX,)=glob_wildcards("/path/to/index/{prefix}.1.ht2l")

        hisat2_index=expand("%s.{ix}.ht2l" % HISAT2_INDEX_PREFIX, ix=range(1, 9)),

The first line explicitly specifies the /path/to/index/, the second misses this path. Be consistent, that should fix your problem.

来源：https://stackoverflow.com/questions/59460188/snakemake-hisat2-alignment-of-many-rnaseq-reads-against-many-genomes

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snakemake