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Multiqc: Runs out of order with only SE or PE dataset #9

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pd321 opened this issue May 30, 2020 · 0 comments

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pd321 commented May 30, 2020

If the data is only SE or PE then due to presence of an empty list in the expansion multiqc has no input and thus runs before any other tools.

The following code in qc.smk needs to be fixed

expand(["results/qc/fastqc/{se_sample}_fastqc.html", 
		"results/qc/fastqc/{pe_sample}_{group}_fastqc.html", 
	 "results/qc/flagstat/{sample}.txt"], sample = samples, 
	 se_sample = se_samples, pe_sample = pe_samples, group = ["r1", "r2"],)

pd321 added the bug label

pd321 self-assigned this

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