Code

Pipeline - draft1#1

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Draft

prototaxites wants to merge 45 commits intodevsanger-tol/longreadmag:devfrom d1sanger-tol/longreadmag:d1Copy head branch name to clipboard

+176,952-363

Commits

Commits on Nov 14, 2024

• initial commit

  

  Jim Downie

  committed
  588f034

• Merge pull request #2 from prototaxites/main

  Show description for 32575a8
  prototaxites

  authored
  32575a8

• Updates:

  Show description for 6424840
  prototaxites

  committed
  6424840

Commits on Nov 15, 2024

• Major updates:

  Show description for 5802c55
  prototaxites

  committed
  5802c55

• Bin3C only run when not using conda profile

  prototaxites

  committed
  d22ba41

Commits on Nov 21, 2024

• Fix metator module

  prototaxites

  committed
  5a46e82

• Adds bin refinement with DASTool

  Show description for 36e7c52
  prototaxites

  committed
  36e7c52

• Start adding MAGSCOT

  prototaxites

  committed
  273fc26

Commits on Nov 22, 2024

• Adds:

  Show description for 188136a
  prototaxites

  committed
  188136a

Commits on Nov 27, 2024

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

  Show description for c71d485
  prototaxites

  authored
  c71d485

• Merge branch 'dev' into d1

  prototaxites

  authored
  54788be

• Ignore hmm assets with precommit

  

  Jim Downie

  committed
  a5eff97

• Fix schema

  

  Jim Downie

  committed
  3da20e6

• Fix linting?

  

  Jim Downie

  committed
  c207428

Commits on Nov 28, 2024

• Simplify HMMER inputs

  

  Jim Downie

  committed
  83f586a

• Multi-threaded pyrodigal, update bwamem2_mem

  

  Jim Downie

  committed
  edf5c74

• Remove schema_input.json

  

  Jim Downie

  committed
  a06c90a

• Add BinQC subworkflow

  

  Jim Downie

  committed
  5abd8cd

• Fix linting

  

  Jim Downie

  committed
  df6fcd5

• Emit versions from MAGSCOT

  

  Jim Downie

  committed
  422b125

• Update test config

  

  Jim Downie

  committed
  ef3700c

• Fix missing operator

  

  Jim Downie

  committed
  2683775

• Add full test, enable binqc

  

  Jim Downie

  committed
  0e250d5

• Fix module

  

  Jim Downie

  committed
  e77aaf7

Commits on Nov 29, 2024

• Begin working on Taxonomy WF

  

  Jim Downie

  committed
  4d04658

• Initial pass at taxonomy with CheckM quality filtering

  

  Jim Downie

  committed
  7572fe3

• Rename DASTool bins so to avoid downstream name conflicts

  

  Jim Downie

  committed
  9a3890f

• Fix combine bins for postbinning, DASTool pyrodigal input

  

  Jim Downie

  committed
  f13797b

• Fix param typo

  

  Jim Downie

  committed
  f88023a

• Fix taxonomy WF, add resource requirements for GTDB

  

  Jim Downie

  committed
  c2af30e

• GTDB takes filtered bin channel now

  

  Jim Downie

  committed
  4f9ae2d

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

  committed
  ebec246

• Fix linting, fix dastool input bug

  

  Jim Downie

  committed
  59ede17

• Fix typo

  

  Jim Downie

  committed
  629cdd2

• Fix contig2bin processing

  

  Jim Downie

  committed
  8cef726

Commits on Dec 11, 2024

• Changes:

  Show description for 05c8326
  

  Jim Downie

  committed
  05c8326

Commits on Dec 12, 2024

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

  

  Jim Downie

  committed
  b6f807a

• add skeleton summary process

  

  Jim Downie

  committed
  674b4ad

Commits on Dec 13, 2024

• Adds:

  Show description for 4cac07b
  

  Jim Downie

  committed
  4cac07b

Commits on Dec 18, 2024

• Update metamdbg version; use gzipped bin files

  

  Jim Downie

  committed
  9950440

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

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

  

  Jim Downie

  committed
  9693dd7

Commits on Dec 20, 2024

• Changes:

  Show description for f6db65a
  

  Jim Downie

  committed
  f6db65a

• Fix Prokka container and update MetaBat2 module

  

  Jim Downie

  committed
  3970d41

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

  

  Jim Downie

  committed
  9d3f933