Update for MetaPhlAn 4.2 compatability#67
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MetaPhlAn version 4.2.x introduced changes to how map files are handled, so '--bowtie2out' arg has been changed to '--mapout' Ideally this would be conditional on the version of MetaPhlAn being run.
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The issue is present in HUMAnN 3.9 & HUMAnN 4.0.0a1 (at least) |
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Description
MetaPhlAn version 4.2.x introduced changes to how map files are handled, so '--bowtie2out' arg has been changed to '--mapout'. This patch only modifies the arg for compatibility. Ideally it would be conditional on the version of MetaPhlAn being run.