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Commits on Nov 14, 2024

• initial commit

  

  Jim Downie

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  588f034

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• Merge pull request #2 from prototaxites/main

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• Updates:

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Commits on Nov 15, 2024

• Major updates:

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• Bin3C only run when not using conda profile

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Commits on Nov 21, 2024

• Fix metator module

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• Adds bin refinement with DASTool

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• Start adding MAGSCOT

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Commits on Nov 22, 2024

• Adds:

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Commits on Nov 27, 2024

• Merge pull request #2 from sanger-tol/dev

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• Merge branch 'dev' into d1

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• Ignore hmm assets with precommit

  

  Jim Downie

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  a5eff97

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• Fix schema

  

  Jim Downie

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  3da20e6

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• Fix linting?

  

  Jim Downie

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Commits on Nov 28, 2024

• Simplify HMMER inputs

  

  Jim Downie

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  83f586a

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• Multi-threaded pyrodigal, update bwamem2_mem

  

  Jim Downie

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  edf5c74

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• Remove schema_input.json

  

  Jim Downie

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  a06c90a

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• Add BinQC subworkflow

  

  Jim Downie

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  5abd8cd

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• Fix linting

  

  Jim Downie

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  df6fcd5

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• Emit versions from MAGSCOT

  

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  422b125

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• Update test config

  

  Jim Downie

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  ef3700c

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• Fix missing operator

  

  Jim Downie

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• Add full test, enable binqc

  

  Jim Downie

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• Fix module

  

  Jim Downie

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Commits on Nov 29, 2024

• Begin working on Taxonomy WF

  

  Jim Downie

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• Initial pass at taxonomy with CheckM quality filtering

  

  Jim Downie

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  7572fe3

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• Rename DASTool bins so to avoid downstream name conflicts

  

  Jim Downie

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  9a3890f

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• Fix combine bins for postbinning, DASTool pyrodigal input

  

  Jim Downie

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  f13797b

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• Fix param typo

  

  Jim Downie

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  f88023a

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• Fix taxonomy WF, add resource requirements for GTDB

  

  Jim Downie

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  c2af30e

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• GTDB takes filtered bin channel now

  

  Jim Downie

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Commits on Dec 6, 2024

• Refine bin processin & dastool bin renaming; adds gtdb_to_ncbi script from GTDB-Tk repo to convert taxonomy

  

  Jim Downie

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  ebec246

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• Fix linting, fix dastool input bug

  

  Jim Downie

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  59ede17

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• Fix typo

  

  Jim Downie

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  629cdd2

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• Fix contig2bin processing

  

  Jim Downie

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Commits on Dec 11, 2024

• Changes:

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Commits on Dec 12, 2024

• Fix linting, update dastool + metabat2 modules, fix renamed modules

  

  Jim Downie

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  b6f807a

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• add skeleton summary process

  

  Jim Downie

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Commits on Dec 13, 2024

• Adds:

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Commits on Dec 18, 2024

• Update metamdbg version; use gzipped bin files

  

  Jim Downie

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Commits on Dec 19, 2024

• Add Prokka to identify ncRNAs for QC purposes; add prokka summary to bin summary process; refactor bin summary code

  

  Jim Downie

  committed
  62bf7a4

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• Add enable_prokka to schema and patch changes to Prokka module (will be reverted when module PR merged)

  

  Jim Downie

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Commits on Dec 20, 2024

• Changes:

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• Fix Prokka container and update MetaBat2 module

  

  Jim Downie

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  3970d41

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• Add basic description to README, fix remote YAML in test

  

  Jim Downie

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  9d3f933

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Commits on Jan 6, 2025

• Add tRNAscan-SE and Infernal to replace Prokka for ncRNA-checking

  

  Jim Downie

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  c94be17

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Commits on Jan 7, 2025

• Fix bugs

  

  Jim Downie

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  cb720e9

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• Merge branch 'rna' into d1

  

  Jim Downie

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Commits on Jan 9, 2025

• Update README.md

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Commits on Jan 10, 2025

• Adds:

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• Fix linting

  

  Jim Downie

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  bab4d0e

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• Update schema

  

  Jim Downie

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  747326a

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• Fix schema

  

  Jim Downie

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  4c6af95

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Commits on Jan 16, 2025

• Merge branch 'dev' into d1

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  fdcd41f

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• Update assembly.nf

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  f8bdfdf

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• Fix pipeline schema

  

  Jim Downie

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  ba97b94

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• Fix test data path

  

  Jim Downie

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  8a54f79

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• Fix schema

  

  Jim Downie

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  adc83e8

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• Fix typo in path

  

  Jim Downie

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Commits on Jan 17, 2025

• Add documentation and apply suggestions from code review.

  

  Jim Downie

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  c21a4be

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• Fix linting

  

  Jim Downie

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  616ec19

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• Prettier on documentation

  

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• Apply suggestions from code review

  

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• Apply suggestions from code review

  

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  bb77ecd

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• Fix publishDir directive

  

  Jim Downie

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  03ffc4e

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Commits on Jan 24, 2025

• Update DAS_Tool image to remove defaults dependency

  

  Jim Downie

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  0a13bea

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Commits on Feb 3, 2025

• Add TreeVal-style CRAM chunking for Hi-C read mapping

  

  Jim Downie

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  0786837

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• Fix bugs

  

  Jim Downie

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  3c6d4d9

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• Merge pull request #14 from sanger-tol/chunk_mapping

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• Remove deleted process from config

  

  Jim Downie

  committed
  1e38b8a

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• Process input YAML using process for output caching

  

  Jim Downie

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  89ac6a2

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• Fix linting

  

  Jim Downie

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  30501cb

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Commits on Feb 4, 2025

• Remove deprecated subWF and rename YAML_INPUT to READ_YAML

  

  Jim Downie

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  302678b

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• Fix unrenamed channel

  

  Jim Downie

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  fe4c60d

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• Template merge 3.2.0

  

  Jim Downie

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  d4fbf31

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• Fix channel

  

  Jim Downie

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  f248455

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• Move local subworkflows to own directories

  

  Jim Downie

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  01f15d3

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• Fix linting errors in local modules by removing switch statements

  

  Jim Downie

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  c4bfff9

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Commits on Feb 5, 2025

• Remove for loop from read mapping subWF

  

  Jim Downie

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  b7a5335

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• Fix languageserver syntax flags

  

  Jim Downie

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  e73ac2e

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• Remove extraneous if from assembly workflow

  

  Jim Downie

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  468067d

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• Move DB preparation to pipeline initialisation subWF

  

  Jim Downie

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  ce670ab

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• Fix GTDB-Tk metadata files to specific versions

  

  Jim Downie

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  cedb870

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• Update schema

  

  Jim Downie

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  a1b960a

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• Correct path to .crai when finding indexes

  

  Jim Downie

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  6061fd0

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• Reduce size of cram chunk in CI test to force chunking

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Commits on Feb 6, 2025

• Update metamdbg/asm

  

  Jim Downie

  committed
  76462a1

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• Fix CRAM chunking as was only aligning the first chunk; Add minumum bin size parameter (currently only for MetaBat2 and Bin3C) delimiting the minumum size of bin allowed in basepairs

  

  Jim Downie

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  ee0592d

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• Add resource requirements for intensive processes

  

  Jim Downie

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  9e03ce3

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• Add .vscode/ to gitignore and remove stray directory

  

  Jim Downie

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  43fc4a0

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• Fix GTDB-Tk database input

  

  Jim Downie

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  8a6def1

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• Update schema

  

  Jim Downie

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  b162a02

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• Add local test YAML input files + use new tolit testdata file paths

  

  Jim Downie

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  66fc249

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Commits on Feb 11, 2025

• Fix GTDB-Tk database input (take 2)

  

  Jim Downie

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