Hi everyone,

Trying to change my habits from bash scripting to snakemake. I struggle to understand the basic logic of few things and the most important one is how to deal with input name. I don't want to freeze a particular input name inside the snakefile, I want it to be able to work on any fastq file, and I know that's what is snakemake for. So I thought the correct way to do this was to use the wildcardss so it know where he have to look and what for (a fastq file for example).

I have made the following script :

from Bio import SeqIO
import sys
import pandas

rule split_fastq:
    input:
        "data/{reads}.fastq",
        "data/{seqsum}.txt"
    output:
        "split_fastq/low.fastq",
        "split_fastq/high.fastq"
    run:
        cols = ["read_id","mean_qscore_template"]
        dataInter = pandas.read_csv(filepath_or_buffer=args.seqsum_path,sep="\t",usecols=cols)
        data = dataInter.rename(mapper={"mean_qscore_template": "quals"}, axis="columns").set_index("read_id").to_dict()["quals"]
        with open("split_fastq/low.fastq",'w+') as a, open("split_fastq/high.fastq",'w+') as b:
            try:
                for rec in SeqIO.parse("data/{reads}.fastq","fastq"):
                    if(data[rec.id] <= 6):
                        SeqIO.write(rec,a,"fastq")
                    else:
                        SeqIO.write(rec,b,"fastq")
            except KeyError:
                sys.exit('\nERROR: Mismatch between sequencing_summary and fastq file: {} was not found in the summary file.\nByeBye.'.formatrec.id))

And I keep switching from this error :

(snakemake-4.8.0_venv) |sbsuser@genologin2 /work/sbsuser/test/roxane/alignement-ont|$snakemake
Building DAG of jobs...
WildcardError in line 5 of /work/sbsuser/test/roxane/alignement-ont/Snakefile:
Wildcards in input files cannot be determined from output files:
'reads'

So then I add the wildcars also in the output like this "split_fastq/{reads}-low.fastq","split_fastq/{reads}-high.fastq" and I end up with :

(snakemake-4.8.0_venv) |sbsuser@genologin2 /work/sbsuser/test/roxane/alignement-ont|$snakemake
Building DAG of jobs...
WorkflowError:
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.

Can someone explain what I am doing wrong ? I really don't get it...

Thanks,

Roxane