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[WIP] A request to remove wort dependecies in database workflow design #6

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[WIP] A request to remove wort dependecies in database workflow design #6

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@ccbaumler ccbaumler commented Jun 14, 2024 •
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In this PR I aimed to create workflows with @bluegenes's directsketch to eliminate the wort directory dependency from sourmash's database workflows.

  • genbank-workflow contains two separate workflows to create new genbank sourmash databases or update existing genbank sourmash databases
  • allthebacteria contains a single workflow that creates new AllTheBacteria sourmash databases

Both workflows contain a test function by changing the output_directory of the config file to test

Remaining TODO:

  • Change allthebacteria test from 1 to 5
  • Include individual README for the workflows
  • Create a GTDB workflow

ccbaumler added 29 commits June 14, 2024 13:22
@ccbaumler
updating to remove wort dependancy
81d8b2d
@ccbaumler
removing duplicates
8fc64e3
@ccbaumler
Add --profile settings and rough README
e3162a0
@ccbaumler
Random sample from 1 to 5 in allthebacteria workflow
3979812
@ccbaumler
initial gtdb workflows (only tax right now)
2cc3d62
@ccbaumler
general manifest handling and workflow streamlined with collection an…
a183f8f 
…d check
@ccbaumler
add a generator and consolidate functions in update_sourmash script
45dfa7e
@ccbaumler
streamline update workflow and improve update_sourmash_dbs script
acb9e38
@ccbaumler
remove unused rule and improve script
572c9a1
@ccbaumler
adding report template
57a81f0
@ccbaumler
Adding current allthebacteria workflow and scripts
42fab7b
@ccbaumler
genbank workflow and scripts update
b067bb1
@ccbaumler
gtdb workflow and scripts update
e2cb680
@ccbaumler
add script to check for the missing sigs
76e6a69
@ccbaumler
add gtdb workflow report with gather_failed script
1e57c82
@ccbaumler
add genbank workflow reporting and fixing failures
1074b64
@ccbaumler
Add allthebacteria scripts and updates to workflow
940a649
@ccbaumler
update failed script and workflow report
d497f87
@ccbaumler
lineage and ident naming fix
47cc397
@ccbaumler
clean up tax script
18d23b3
@ccbaumler
compatible GTDB manifest and lineage with GCA/GCF format
f2ffbc7
@ccbaumler
Create readme for genbank update
4b4e8e3
@ccbaumler
update readme for genbank update
eb7d03a
@ccbaumler
Add the output files from the workflow
f02cad5
@ccbaumler
Fixes lineage bug - creates old lineage and new lineage files
31ef9d7
@ccbaumler
update atb for lineage and cleaner final repo
5f948c3
@ccbaumler
rm extra snakefile and config
5fa453a
@ccbaumler
adding context to IOFileException error
2f1d456
@ccbaumler
add function and unpack in single manifest rules
795ce73
@ccbaumler ccbaumler mentioned this pull request Apr 14, 2025
Closed
@ccbaumler ccbaumler mentioned this pull request Aug 13, 2025
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@ccbaumler