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Fix input path to s3://omic/eureka/prodigy/*.pdb
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This commit is contained in:
Olamide Isreal
2026-03-17 16:44:26 +01:00
parent 19fd443501
commit c8fd6b4084
4 changed files with 5 additions and 6 deletions
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1
.gitignore vendored
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@@ -10,4 +10,3 @@ __pycache__/
.idea/ .idea/
*.tmp *.tmp
*.swp *.swp
tests/test_data/dataset.tgz

2
main.nf
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@@ -3,7 +3,7 @@
nextflow.enable.dsl=2 nextflow.enable.dsl=2
// Default parameters // Default parameters
params.pdb = 's3://omic/eureka/prodigy/input/*.pdb' params.pdb = 's3://omic/eureka/prodigy/*.pdb'
params.outdir = 's3://omic/eureka/prodigy/output' params.outdir = 's3://omic/eureka/prodigy/output'
params.distance_cutoff = 5.5 params.distance_cutoff = 5.5
params.acc_threshold = 0.05 params.acc_threshold = 0.05

2
nextflow.config
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@@ -15,7 +15,7 @@ manifest {
// Global default parameters // Global default parameters
params { params {
pdb = 's3://omic/eureka/prodigy/input/*.pdb' pdb = 's3://omic/eureka/prodigy/*.pdb'
outdir = 's3://omic/eureka/prodigy/output' outdir = 's3://omic/eureka/prodigy/output'
distance_cutoff = 5.5 distance_cutoff = 5.5
acc_threshold = 0.05 acc_threshold = 0.05

6
params.json
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@@ -3,13 +3,13 @@
"pdb": { "pdb": {
"type": "file", "type": "file",
"description": "Path to input PDB or mmCIF structure file(s) for binding affinity prediction", "description": "Path to input PDB or mmCIF structure file(s) for binding affinity prediction",
"default": "s3://omic/eureka/prodigy/input/*.pdb", "default": "s3://omic/eureka/prodigy/*.pdb",
"required": true, "required": true,
"pipeline_io": "input", "pipeline_io": "input",
"var_name": "params.pdb", "var_name": "params.pdb",
"examples": [ "examples": [
"s3://omic/eureka/prodigy/input/3bzd.pdb", "s3://omic/eureka/prodigy/3bzd.pdb",
"s3://omic/eureka/prodigy/input/*.pdb" "s3://omic/eureka/prodigy/*.pdb"
], ],
"pattern": ".*\\.(pdb|cif)$", "pattern": ".*\\.(pdb|cif)$",
"enum": [], "enum": [],