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[Metagenomics Illumina] fix to single-end problem when running with new setup#79

Draft
AstrobioMike wants to merge 1 commit intonasa:metagenomicsfrom
AstrobioMike:patch-5
Draft

[Metagenomics Illumina] fix to single-end problem when running with new setup#79
AstrobioMike wants to merge 1 commit intonasa:metagenomicsfrom
AstrobioMike:patch-5

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@AstrobioMike
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Draft currently until i get confirmation this fixed it from the individual who hit the issue.

  • fix to single-end humann3 run where the ref db for metaphlan needs to be explicitly specified
    • this wasn't always necessary, but it became so a little while back. A fix was already implemented for paired-end, but apparently i didn't catch it for single-end (and it wouldn't cause a problem unless it was the first time a workflow was run on a new system)
    • I have this marked as a draft to be left alone until i get confirmation from Ankur Naqib (works with Stefan Green at Rush) that this solved the issue for him
      • once that's confirmed, i'll update here

- fix to single-end humann3 run where the ref db needs to be explicitly specified  - this wasn't always necessary, but it became so a little while back. a fix was already implemented for paired-end, but apparently i didn't catch it for single-end (and it wouldn't cause a problem unless it was the first time a workflow was run on a new system)
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@AstrobioMike

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