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Add RoseTTAFold-All-Atom #220

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Add RoseTTAFold-All-Atom #220

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@jscgh jscgh commented Nov 20, 2024 •
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Adds RoseTTAFold-All-Atom as a module per #197.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

nbtm-sh and others added 30 commits July 29, 2024 13:32
@nbtm-sh
feat(katana.config): Created file katana.config
aa9be9f
@nbtm-sh
feat(katana.config): Added params for PBS queues
678b212
@nbtm-sh
feat(katana.config): Added executor parameter to allow the use Katana…
82466e0 
… scheduler
@nbtm-sh
feat(katana.config): Added label configs for pushing to GPU partition
8d2a771
@nbtm-sh
Merge pull request #1 from Australian-Structural-Biology-Computing/cr…
1ad4996 
…eate-katana-config

Create Katana config
@nbtm-sh
feat(run_alphafold2): Added 'gpu_compute' label to the Alphafold process
3c1fb28
@nbtm-sh
Merge pull request #2 from Australian-Structural-Biology-Computing/ad…
67704b4 
…d-labels-to-gpu-processes

Add labels to GPU processes
@nbtm-sh
feat(run_alphafold2_pred): Added 'gpu_compute' label
e8d2abb
@nbtm-sh
Merge pull request #3 from Australian-Structural-Biology-Computing/ad…
2021623 
…d-labels-to-gpu-processes

Add GPU Compute label
@nbtm-sh
revert(run_alphafold2.nf): Removed GPU compute label from pipeline
13dd1cb
@nbtm-sh
Merge pull request #4 from Australian-Structural-Biology-Computing/ad…
b0d483e 
…d-labels-to-gpu-processes

Remove GPU Compute label from CPU pipeline
@jscgh
Updated database links
2444395 
	modified:   conf/dbs.config
	modified:   modules/local/run_alphafold2.nf
Added variable links in dbs.config and run_alphafold2.nf
@jscgh
Merge pull request #6 from Australian-Structural-Biology-Computing/da…
4ce2e18 
…tabase

Updated database links
@nbtm-sh
feat(pf_files): Added testing files
8b9452a
@nbtm-sh
Merge branch 'unsw-dev' into add-testing-files
32311ba
@nbtm-sh
Merge pull request #7 from Australian-Structural-Biology-Computing/ad…
e676c33 
…d-testing-files

Add testing files
@nbtm-sh
fix(proteinfold_test.sh): Made path to main.nf rel
0962f91
@nbtm-sh
revert(base.config): Changed executor back to local for testing as cl…
992d6d1 
…uster tooling is incomlete
@nbtm-sh
fix(proteinfold_test.sh): Changed mode to 'split_msa_production'
32d466c
@ziadbkh
Merge pull request #2 from nf-core/master
d135dc8 
Sync master branch
@nbtm-sh
fix(dbs.conf): Updated dbs.conf to work on UNSW infrastructure
b3140e7
@nbtm-sh
fix(run_alphafold2_msa): Fixed incorrectly named files
4047e62
@nbtm-sh
fix(run_alphafold2_pred): Fixed incorrectly named files
93513bc
@nbtm-sh
fix(proteinfold_test.sh): Added singulairty argument
a007d5a
@nbtm-sh
fix(samplesheet): Changed sample to a much smaller sample
232c8c9
@nbtm-sh
fix(samplesheet): Changed sampel to a smaller sample
03f2575
@nbtm-sh
Merge pull request #8 from Australian-Structural-Biology-Computing/ad…
632610b 
…d-dbs-variables-to-msa-pipeline

Make pipeline work on UNSW Katana
@nbtm-sh
feat(conf/dbs): Added variables for database names, and file names
964f5d0
@nbtm-sh
feat(conf/dbs): Changed config paths to use database variables instea…
2a79fe4 
…d of hardcoded values
@nbtm-sh
feat(run_alphafold2): Changed hardcoded paths to use variables and up…
c218ad2 
…dated variable names
@jscgh jscgh changed the title [WIP] Add RoseTTAFold-All-Atom Add RoseTTAFold-All-Atom Nov 27, 2024
@jscgh jscgh marked this pull request as ready for review November 27, 2024 04:22
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3 participants
@jscgh @nbtm-sh @ziadbkh