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feat: expose FDR conservative parameter #690

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Merged
ypriverol merged 2 commits into from
Apr 4, 2026
Merged

feat: expose FDR conservative parameter #690

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3344e87
feat: expose FDR conservative parameter for FalseDiscoveryRate
ypriverol Apr 3, 2026
48937af
chore: update quantms-rescoring container to 0.0.16
ypriverol Apr 3, 2026
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1 change: 1 addition & 0 deletions modules/local/openms/false_discovery_rate/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ process FALSE_DISCOVERY_RATE {
-FDR:PSM ${params.run_fdr_cutoff} \\
-algorithm:add_decoy_peptides \\
-algorithm:add_decoy_proteins \\
-algorithm:conservative ${params.fdr_conservative} \\
$args \\
2>&1 | tee ${id_file.baseName}_fdr.log

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4 changes: 2 additions & 2 deletions modules/local/utils/msrescore_features/main.nf
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Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"

input:
tuple val(meta), path(idxml), path(mzml), path(model_weight), val(search_engine)
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4 changes: 2 additions & 2 deletions modules/local/utils/msrescore_fine_tuning/main.nf
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Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"

input:
tuple val(meta), path(idxml), path(mzml), val(groupkey), path(ms2_model_dir)
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4 changes: 2 additions & 2 deletions modules/local/utils/psm_clean/main.nf
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Expand Up @@ -3,8 +3,8 @@ process PSM_CLEAN {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"

input:
tuple val(meta), path(idxml), path(mzml)
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4 changes: 2 additions & 2 deletions modules/local/utils/spectrum_features/main.nf
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Expand Up @@ -3,8 +3,8 @@ process SPECTRUM_FEATURES {
label 'process_low'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"

input:
tuple val(meta), path(id_file), val(search_engine), path(ms_file)
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -31,6 +31,7 @@ params {
run_fdr_cutoff = 0.10
protein_level_fdr_cutoff = 0.01
psm_level_fdr_cutoff = 0.01
fdr_conservative = true // Use (D+1)/T formula (true) or (D+1)/(T+D) (false) for FDR estimation
psm_clean = false

// Debug level
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -966,6 +966,13 @@
"fa_icon": "fas fa-filter",
"help_text": "After applying protein-level FDR cutoff, this additionally filters PSMs to be used for quantification and reporting."
},
"fdr_conservative": {
"type": "boolean",
"description": "Use conservative FDR formula (D+1)/T instead of (D+1)/(T+D). Default: true",
"default": true,
"fa_icon": "fas fa-shield-alt",
"help_text": "When true, uses the conservative formula (D+1)/T for FDR estimation, which provides an upper bound on the true FDR. When false, uses (D+1)/(T+D) which gives a tighter estimate. See Keich & Noble (2025, Nature Methods) for details on FDR estimation methods."
},
"protein_inference_debug": {
Comment on lines +975 to 976

@qodo-code-review qodo-code-review Bot Apr 3, 2026

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1. Invalid schema json 🐞 Bug ≡ Correctness

nextflow_schema.json is syntactically invalid because the newly added fdr_conservative property
block is not followed by a comma even though additional properties follow. Any consumer parsing the
schema will fail (e.g., nf-core launch / parameter schema validation tooling).
Agent Prompt 
## Issue description
`nextflow_schema.json` is invalid JSON because the `fdr_conservative` property definition is not followed by a comma, but another property (`protein_inference_debug`) follows immediately after.

## Issue Context
This breaks JSON parsing for any tooling that reads `nextflow_schema.json`.

## Fix
Add a trailing comma after the closing brace of the `fdr_conservative` property block.

## Fix Focus Areas
- nextflow_schema.json[969-976]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

"type": "integer",
"description": "Debug level for the protein inference step. Increase for verbose logging",
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