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Pipeline - draft1 #1

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@prototaxites prototaxites commented Nov 26, 2024 •
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Adds:

  • Input from YAML
  • Assembly
    • metaMDBG
    • assembly statistics/num circular
  • Read mapping to assembly - hi-c and pacbio
  • Binning with
    • metabat2
    • maxbin2
    • bin3c
    • metator
  • Bin refinement
    • gene prediction with pyrodigal
    • magscot
    • dastool
  • Bin QC
    • Checkm
    • Seqkit statistics
    • infernal + trnascan-se - count trnas
  • Taxonomy
    • GTDBTk
    • TaxKit - get NCBI taxids
  • Summary
    • assembly statistics
    • bin statistics and scoring

Jim Downie and others added 9 commits November 14, 2024 14:23
initial commit
588f034
@prototaxites
Merge pull request #2 from prototaxites/main
32575a8 
add co2footprint
@prototaxites
Updates:
6424840 
- Add sketch binning subworkflow
- Map reads + hic to reference
- Patch read mapping modules so they output the meta object
from the reference
- Calculate depths
@prototaxites
Major updates:
5802c55 
- binnng workflow has metabat2,maxbin2 and bin3c
- bin3c modules
- read hic enzymes input from YAML
- move hic cram preprocessing to new PREPARE_DATA workflow

Minor updates:
- Patch MaxBin2 to emit ungzipped fasta
@prototaxites
Bin3C only run when not using conda profile
d22ba41
@prototaxites
Fix metator module
5a46e82
@prototaxites
Adds bin refinement with DASTool
36e7c52 
Skeleton of binning with Metator - needs uncontaminated container to
    continue.
@prototaxites
Start adding MAGSCOT
273fc26
@prototaxites
Adds:
188136a 
    - Bin refinement with Magscot

Fixes:
    - Binning with Metator now functional
@prototaxites prototaxites self-assigned this Nov 26, 2024
@prototaxites prototaxites marked this pull request as ready for review November 26, 2024 15:52
@prototaxites
Merge pull request #2 from sanger-tol/dev
c71d485 
Merge pull request #1 from prototaxites/main
prototaxites added a commit that referenced this pull request Nov 27, 2024
@prototaxites
Merge pull request #1 from prototaxites/main
5ee4f4a 
add co2footprint
@prototaxites prototaxites changed the title Pipeline skeleton - input, assembly, binning and bin refinement Pipeline - draft1 Nov 28, 2024
Jim Downie and others added 8 commits January 6, 2025 16:58
Add tRNAscan-SE and Infernal to replace Prokka for ncRNA-checking
c94be17
Fix bugs
cb720e9
Merge branch 'rna' into d1
59edad5
@prototaxites
Update README.md
eeba4a2
Adds:
263769c 
- circular contig counting
    - counts circular contigs using custom module
    - custom genome stats module that incorporates circular counts
- basic bin scoring
- new bin summary output - per group summary
- remove collate_bins parameter and just collate bins for gtdbtk an
  checkm2
Fix linting
bab4d0e
Update schema
747326a
Fix schema
4c6af95
@prototaxites prototaxites marked this pull request as ready for review January 16, 2025 15:10
weaglesBio
weaglesBio reviewed Jan 17, 2025
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weaglesBio
weaglesBio requested changes Jan 17, 2025
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Looking good, just need to resolve a few comments.

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@weaglesBio weaglesBio weaglesBio requested changes

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@prototaxites @sanger-tolsoft @weaglesBio