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Dev -> Main for 0.2.0 release #16

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merged 49 commits into from
Dec 3, 2024
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39e3d52
Exposed additional chai-1 parameters to Nextflow.
FloWuenne Nov 28, 2024
bd491fb
Updated changelog.
FloWuenne Nov 28, 2024
bab3a0c
Fix changelog formatting.
FloWuenne Nov 28, 2024
dceee4c
Fixed params definitions for CHAI_1 process.
FloWuenne Nov 28, 2024
6563356
Add log for GPU/CPU
adamrtalbot Nov 28, 2024
3f059cc
Apply suggestions from code review
drpatelh Nov 28, 2024
33f0a0e
fix: update params being passed to NF_CHAI workflow
drpatelh Nov 28, 2024
ec0a0f5
[chore]: update CHANGELOG
drpatelh Nov 28, 2024
de649d7
Merge pull request #11 from FloWuenne/add_chai1_params
drpatelh Nov 28, 2024
39d1a36
Merge pull request #12 from adamrtalbot/patch-1
drpatelh Nov 28, 2024
e443420
chore: fix entries in CHANGELOG
drpatelh Nov 28, 2024
a37ad6b
chore: bump pipeline version to 0.2.0
drpatelh Nov 28, 2024
ce0143b
chore: fix entries in CHANGELOG
drpatelh Nov 28, 2024
00d2bb5
docs: make POC language more explicit
drpatelh Nov 28, 2024
dd940d5
feat: bump chai_lab version to 0.4.2
drpatelh Nov 28, 2024
c58c4bb
feat: bump container for chai_lab 0.4.2
drpatelh Nov 28, 2024
668cd9e
chore: update CHANGELOG
drpatelh Nov 28, 2024
213164d
Merge pull request #13 from seqeralabs/bump_chai
drpatelh Nov 28, 2024
1739592
feat: Added msa parameter.
FloWuenne Nov 29, 2024
489727f
Fix: Remove local path from config.
FloWuenne Nov 29, 2024
4723a3d
Fix: Added CHAI_DOWNLOADS_DIR back into module.
FloWuenne Nov 29, 2024
6f6a137
fix: Removed resource label from CHAI_1 and added groundswell optimiz…
FloWuenne Nov 29, 2024
75e9ed9
fix: Added apptainer gpu config runOption.
FloWuenne Nov 29, 2024
0022e02
fix: set output-dir param to meta.id again
FloWuenne Nov 29, 2024
bd2aa5e
fix: changed torch device definition back, to work on cpu only machines.
FloWuenne Nov 29, 2024
0056f46
fix: Fixed indentation in config.
FloWuenne Nov 29, 2024
3744488
fix: Added Path to msa_dir in run_chai_1.py
FloWuenne Nov 29, 2024
f8208e4
fix: Fixed indentation and quotes for defs in CHAI_1
FloWuenne Nov 29, 2024
9f21620
fix: Add exception in run_chai_1.py for case that msa is not provided.
FloWuenne Nov 29, 2024
67b5b99
fix: Updated nextflow_schema.json.
FloWuenne Nov 30, 2024
14db704
chore: Updated changelog.
FloWuenne Nov 30, 2024
33c0d85
fix: Fixed left padding in nextflow.config
FloWuenne Nov 30, 2024
915fe50
fix: Fixed msa_dir param input for run_chai_1.py
FloWuenne Nov 30, 2024
80b206b
chore: update CHANGELOG
drpatelh Dec 2, 2024
48665f5
chore: rename underscores to dashes in Python script for consistency
drpatelh Dec 2, 2024
816b2b6
chore: move --msa_dir param up in schema and add appropriate fields
drpatelh Dec 2, 2024
7ebaddb
chore: move --msa_dir param up in parameter priority as input
drpatelh Dec 2, 2024
a0559bc
fix: bug in fasta file name
drpatelh Dec 2, 2024
9b40231
chore: change some variable names in main module
drpatelh Dec 2, 2024
9c5bc4a
fix: revert removal of process_high label
drpatelh Dec 2, 2024
3b26c20
docs: add sentence about --msa_dir to main README
drpatelh Dec 2, 2024
17a6f52
Merge pull request #14 from seqeralabs/add_msa_param
drpatelh Dec 2, 2024
5711870
chore: move test data for pipeline into own folder
drpatelh Dec 2, 2024
df104d2
feat: add new test data for MSAs
drpatelh Dec 2, 2024
b24624b
fix: update paths for test data in configs
drpatelh Dec 2, 2024
5c1c520
feat: add test_full_msa profile
drpatelh Dec 2, 2024
ac88955
chore: update CHANGELOG
drpatelh Dec 2, 2024
cbd9677
docs: add sources for test data
drpatelh Dec 3, 2024
191da24
Merge pull request #15 from seqeralabs/add_msa_test_profile
drpatelh Dec 3, 2024
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fix: update params being passed to NF_CHAI workflow
drpatelh authored Nov 28, 2024

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commit 33f0a0e2a113dd35a817db87cd3ccb4839bc05bc
6 changes: 5 additions & 1 deletion main.nf
Original file line number Diff line number Diff line change
@@ -43,7 +43,11 @@ workflow {
//
NF_CHAI (
params.input,
params.weights_dir
params.weights_dir,
params.num_trunk_recycles,
params.num_diffusion_timesteps,
params.seed,
params.use_esm_embeddings
)

//