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feature: subworkflow for isolate genomes #127

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feature: subworkflow for isolate genomes #127

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@franciscozorrilla franciscozorrilla commented Jun 9, 2023 •
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馃 Isolate genomes subworkflow 馃敠

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

馃悕 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

馃敤 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

@franciscozorrilla
feature: add shovill rule to Snakefile
7452739 
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
@franciscozorrilla
Update Snakefile
23fa499 
remove unnecessary code and move shovill rule up to a more appropriate place in the Snakefile
@franciscozorrilla
faet: add new drep_isolate rule
52ae545
@franciscozorrilla franciscozorrilla changed the title feature: add shovill support for metaGEM feature: subworkflow for isolate genomes Jun 9, 2023
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