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feature: subworkflow for isolate genomes - #127

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franciscozorrilla-shovill-patch
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feature: subworkflow for isolate genomes#127
franciscozorrilla wants to merge 3 commits into
masterfrom
franciscozorrilla-shovill-patch

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@franciscozorrilla

@franciscozorrilla franciscozorrilla commented Jun 9, 2023

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🦠 Isolate genomes subworkflow 🔦

Adding support for isolate genome assembly in the next version of metaGEM 💎

🐍 Snakefile tasks

  • create shovill rule for dealing with isolate assembly data
  • create dRep rule for derelplicating megahit assembly, metaGEM-reassembled bin, and shovill output to select best genome
  • create helper rule to populate drep input from corresponding input subfolders

🔨 Additional modifications for full integration/support

  • metaGEM.sh: add options + support for new tasks
  • config.yaml: add params used in new tasks
  • config readme file: add new perl environment for shovill (to also include prokka, roary, etc.), dRep could go in main metaGEM env
  • conda recipe: update
  • main readme file: text and eventually figure

add shovill rule to Snakefile for dealing with isolate assembly data. will also need to make additions/changes to
* metaGEM.sh: add flag/option to support new task
* config.yaml: add params used in task
* readme file: text and eventually figure
@franciscozorrilla franciscozorrilla self-assigned this Jun 9, 2023
@franciscozorrilla franciscozorrilla added enhancement New feature or request method Novel or alternative conceptual method labels Jun 9, 2023
remove unnecessary code and move shovill rule up to a more appropriate place in the Snakefile
@franciscozorrilla franciscozorrilla changed the title feature: add shovill support for metaGEM feature: subworkflow for isolate genomes Jun 9, 2023
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