Snakemake : "wildcards in input files cannot be determined from output files"

Question

I use Snakemake to execute some rules, and I've a problem with one:

rule filt_SJ_out:
input: 
    "pass1/{sample}SJ.out.tab"

output:
    "pass1/SJ.db"

shell:''' 
gawk '$6==1 || ($6==0 && $7>2)' {input} >> {output};


'''

Here, I just want to merge some files into a general file, but by searching on google I've see that wildcards use in inputs must be also use in output.

But I can't find a solution to work around this problem ..

Thank's by advance

Answer 1

If you know the values of sample prior to running the script, you could do the following:

SAMPLES = [... define the possible values of `sample` ...]

rule filt_SJ_out:
    input: 
        expand("pass1/{sample}SJ.out.tab", sample=SAMPLES)
    output:
        "pass1/SJ.db"
    shell:
        """ 
        gawk '$6==1 || ($6==0 && $7>2)' {input} >> {output};
        """

In the input step, this will generate a list of files, each of the form pass1/<XYZ>SJ.out.tab.