This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Snakemake: output folder a as dependency to a different rule

I want to make sure a genome is indexed by STAR before I use STAR to align the genome.

Currently, I have two rules to achieve this:

rule star_index:
    input:
        gtf = "path/to/gtfFile.gtf",
        fasta = "path/to/assembly.fa"
    output:
        directory("path/to/star/index/directory")
    message:
        "Building STAR Index"
    wrapper:
        "0.36.0/bio/star/index"

rule align_to_genome:
    input: 
        fq1 = "path/to/fastq_forward",
        fq2 = "path/to/fastq_reverse"
    output:
        "star/{sample}/Aligned.out.bam",
        "star/{sample}/ReadsPerGene.out.tab"
    log:
        "logs/star/{sample}.log"
    params:
        index="path/to/star/index/directory"
    wrapper:
        "0.31.1/bio/star/align"

This currently works, but the genome index isn't a dependancy to the mapping, so if it's missing the mapping just fails (whereas I'd want the index to be built). Is the only thing to do to manually specify all the output files of STAR index (and then re-write the wrapper to only use the folder name in the star index command?) That seems quite clunky, as STAR outputs its index to a folder, and also accepts the index as a folder.

snakemake rna-seq
• 6,747 views • link
updated by gb gb • written by Veewhy • Veewhy

1 answer

Something like this:

rule star_index:
    input:
        gtf = "path/to/gtfFile.gtf",
        fasta = "path/to/assembly.fa"
    output:
        dir = directory("path/to/star/index/directory")
    message:



 rule align_to_genome:
        input: 
            dir = rules.star_index.output.dir
            fq1 = "path/to/fastq_forward",
            fq2 = "path/to/fastq_reverse"
        output:

Never used the directory output but if it is not possible to do dir = directory("path/to/star/index/directory") You can put one of the output files of star or even create a "fake" file afther the index creation and give that as input to rule align_to_genome

Here the page (with better explanation): https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rule-dependencies

• 0 views • link
written by gb gb

Log in to answer this question.

More posts like this