Not executed fastqc for specified inputs

[nkimoto]

hi. I recently executed this pipeline for my job. But after I ran this pipeline and removed the output of the fastqc, I can't reproduce the output of fastqc (qc/fastqc/A-1.html for example).

After some experiment, I find this is because only first line is recognized as "inputs" by snakemake. So I fixed under the lines from https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/6bde762e80eab54ba5d68681f64b58f66ab963b8/rules/qc.smk#L24-L27

to

    expand("qc/samtools-stats/{u.sample}-{u.unit}.txt", u=units.itertuples())
    expand("qc/fastqc/{u.sample}-{u.unit}.zip", u=units.itertuples())
    expand("qc/dedup/{u.sample}-{u.unit}.metrics.txt", u=units.itertuples())

I can get the expected results. Is this bug of expand module? Please explain what is happend.

[tdido]

Not sure if it's a bug, I've asked in the issue I just opened.

For the time being, the easiest solution is to convert the input to a list:

 expand(["qc/samtools-stats/{u.sample}-{u.unit}.txt", 
         "qc/fastqc/{u.sample}-{u.unit}.zip", 
         "qc/dedup/{u.sample}-{u.unit}.metrics.txt"], 
        u=list(units.itertuples())