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Prepare phylogenetic workflow for Nextclade workflow #57

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merged 2 commits into from
May 24, 2024

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j23414
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@j23414 j23414 commented May 24, 2024

Description of proposed changes

Following the plan laid out in #21 (comment)

This PR is making some minor updates to the phylogenetic workflow to prepare for the Nextclade workflow.

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Checklist

  • Checks pass
  • Check a phylogenetic run (see run here)
genome E gene
all all/genome all/E
denv1 denv1/genome denv1/E
denv2 denv2/genome denv2/E
denv3 denv3/genome denv3/E
denv4 denv4/genome denv4/E

@j23414 j23414 requested a review from a team May 24, 2024 17:57
@@ -73,6 +74,7 @@ rule filter:
--group-by {params.group_by} \
--sequences-per-group {params.sequences_per_group} \
--min-length {params.min_length} \
--include {input.include} \
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  1. is it worth putting this closer to the --exclude option to make it clear both are in play?
  2. is it worth a comment explaining how --exclude and --include interact, or is that assumed to be table-stakes knowledge for anybody that might want to modify this?

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@j23414 j23414 May 24, 2024

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  1. I meant to put --include next to --exclude. I got faked out by --exclude-where, thanks for flagging!
  2. The comments explaining how --exclude and --include interact is mostly pointing to augur filter docs, aka, not commented here. However, when I get into lineage defining strains, the "include.txt" may need to be split out into DENV1-DENV4 and I haven't figured out the design for that yet.

Potential design 1: Keep separate include_{serotype}.txt files

Potential design 2: Create a snakemake rule that takes a lineage.tsv and creates include_{serotype}.txt and append_clade_membership_{serotype}.tsv... I haven't written this up yet.

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assumed to be table-stakes knowledge for anybody that might want to modify this [include.txt]

Actually this is a good point, I went with Potential design 1 as easier to explain to other people. 3ed18d2

Fixup of include next to exclude in c6e589f

Adds a configurable includes_{serotype}.txt to force-include key strains
(e.g. vaccine-related, lineage-defining) for each serotype tree.
@j23414 j23414 force-pushed the 56-prep-phylo-branch-for-nextclade branch from 3ed18d2 to 5af15a1 Compare May 24, 2024 20:26
@j23414 j23414 merged commit 75d9c5f into main May 24, 2024
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@j23414 j23414 deleted the 56-prep-phylo-branch-for-nextclade branch May 24, 2024 21:16
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2 participants