metaphlan3 and strainphlan

Adding rules for first steps of StrainPhlan and add new metaphlan rule for version 3

Closes #21 (closed)

reference

https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0

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• 6cad6524 - move bowtie2out and sams from params to output

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• e60c44c9 - update paired metaphlan with new outputs

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• 3bd54e46 - add sample2markers for strainphlan

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• b265ed7f - mv output dir to params

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For Step 4, we extract markers from metaphlan db for each chosen clade. Therefore, we need to think about what clades we want? automatically fetch all found clades from metaphlan output?

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unmarked as a Work In Progress

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mentioned in commit 18caac99

merged