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Merged
weizhongchun merged 3 commits into from
Dec 30, 2025
Merged

Update main.nf #19

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176678c
Update main.nf
weizhongchun Dec 30, 2025
ad80502
Update test_data.config
weizhongchun Dec 30, 2025
af92ca7
Update main.nf
weizhongchun Dec 30, 2025
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23 changes: 14 additions & 9 deletions modules/bigbio/onsite/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,12 @@ process ONSITE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.mzml_id}"

// Algorithm selection: ascore (default), phosphors, or lucxor
def algorithm = params.onsite_algorithm ?: 'ascore'
// Algorithm selection: lucxor (default), ascore, or phosphors
def algorithm = params.onsite_algorithm ?: 'lucxor'

// Common parameters for all algorithms
def fragment_tolerance = params.onsite_fragment_tolerance ?: '0.05'
def compute_all_scores = params.onsite_compute_all_scores ? '--compute-all-scores' : ''

// Set default value for add_decoys (can be overridden by setting params.onsite_add_decoys = false)
def onsite_add_decoys = params.containsKey('onsite_add_decoys') ? params.onsite_add_decoys : true
Expand All @@ -47,8 +48,8 @@ process ONSITE {
--fragment-mass-tolerance ${fragment_tolerance} \\
--fragment-mass-unit ${fragment_unit} \\
${add_decoys} \\
${debug} \\
${args}
${compute_all_scores} \\
${debug}
"""
} else if (algorithm == 'phosphors') {
// PhosphoRS: uses -in, -id, -out, --fragment-mass-unit
Expand All @@ -61,8 +62,8 @@ process ONSITE {
--fragment-mass-tolerance ${fragment_tolerance} \\
--fragment-mass-unit ${fragment_unit} \\
${add_decoys} \\
${debug} \\
${args}
${compute_all_scores} \\
${debug}
"""
} else if (algorithm == 'lucxor') {
// LucXor: uses -in, -id, -out, --fragment-error-units (note: error-units not mass-unit)
Expand All @@ -74,8 +75,10 @@ process ONSITE {
def max_num_perm = params.onsite_max_num_perm ?: '16384'
def modeling_threshold = params.onsite_modeling_score_threshold ?: '0.95'
def scoring_threshold = params.onsite_scoring_threshold ?: '0.0'
def min_num_psms = params.onsite_min_num_psms_model ?: '50'
def min_num_psms = params.onsite_min_num_psms_model ?: '5'
def rt_tolerance = params.onsite_rt_tolerance ?: '0.01'
def min_psms = params.onsite_min_psms ?: '5'
def disable_split_by_charge = params.onsite_disable_split_by_charge ? '--disable-split-by-charge' : ''

// Optional target modifications - default for LucXor includes decoy
def target_mods = params.onsite_target_modifications ? "--target-modifications ${params.onsite_target_modifications}" : "--target-modifications 'Phospho(S),Phospho(T),Phospho(Y),PhosphoDecoy(A)'"
Expand Down Expand Up @@ -103,8 +106,10 @@ process ONSITE {
--scoring-threshold ${scoring_threshold} \\
--min-num-psms-model ${min_num_psms} \\
--rt-tolerance ${rt_tolerance} \\
${debug} \\
${args}
--min-psms ${min_psms} \\
${disable_split_by_charge} \\
${compute_all_scores} \\
${debug}
"""
} else {
error "Unknown onsite algorithm: ${algorithm}. Supported algorithms: ascore, phosphors, lucxor"
Expand Down
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