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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 30 commits January 17, 2025 16:00
Apply suggestions from code review
bb77ecd
Fix publishDir directive
03ffc4e
Update DAS_Tool image to remove defaults dependency
0a13bea
Add TreeVal-style CRAM chunking for Hi-C read mapping
0786837
Fix bugs
3c6d4d9
@prototaxites
Merge pull request #14 from sanger-tol/chunk_mapping
06a908f 
Chunk mapping
Remove deleted process from config
1e38b8a
Process input YAML using process for output caching
89ac6a2
Fix linting
30501cb
Remove deprecated subWF and rename YAML_INPUT to READ_YAML
302678b
Fix unrenamed channel
fe4c60d
Template merge 3.2.0
d4fbf31
Fix channel
f248455
Move local subworkflows to own directories
01f15d3
Fix linting errors in local modules by removing switch statements
c4bfff9
Remove for loop from read mapping subWF
b7a5335
Fix languageserver syntax flags
e73ac2e
Remove extraneous if from assembly workflow
468067d
Move DB preparation to pipeline initialisation subWF
ce670ab
Fix GTDB-Tk metadata files to specific versions
cedb870
Update schema
a1b960a
Correct path to .crai when finding indexes
6061fd0
@prototaxites
Reduce size of cram chunk in CI test to force chunking
16577d9
Update metamdbg/asm
76462a1
Fix CRAM chunking as was only aligning the first chunk; Add minumum b…
ee0592d 
…in size parameter (currently only for MetaBat2 and Bin3C) delimiting the minumum size of bin allowed in basepairs
Add resource requirements for intensive processes
9e03ce3
Add .vscode/ to gitignore and remove stray directory
43fc4a0
Fix GTDB-Tk database input
8a6def1
Update schema
b162a02
Add local test YAML input files + use new tolit testdata file paths
66fc249
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@prototaxites @sanger-tolsoft @weaglesBio