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Taxonomy: kraken2 on reads: combine PE and SE reads

It seems that only PE reads are used for the kraken2-based taxonomic profiling: kraken_reads_SE.smk is imported only if there is one single metaG input file (see here), otherwise kraken_reads.smk is being imported and it processes only PE reads.

It would more consistent to combine PE and SE reads together.

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Taxonomy: kraken2 on reads: combine PE and SE reads