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@ -173,7 +173,7 @@ def check_samplesheet(file_in, file_out):
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## Auto-detect paired-end/single-end
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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elif sample and fastq_1 and not fastq_2: ## Single-end short reads
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elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif (
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sample and fasta and not fastq_1 and not fastq_2
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