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update onsite #90

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Merged
daichengxin merged 2 commits into from
Jun 14, 2026
Merged

update onsite #90

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647fe38
update onsite
daichengxin Jun 14, 2026
763c00f
Update main.nf
daichengxin Jun 14, 2026
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2 changes: 1 addition & 1 deletion modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"bigbio": {
"onsite": {
"branch": "main",
"git_sha": "18d45a9dd5d4bb5aa915ffe3d264ab6c021ee3c2",
"git_sha": "7be544ac0bb20ea39c8fb46f57c5b8c39e06b183",
"installed_by": ["modules"]
},
"thermorawfileparser": {
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14 changes: 7 additions & 7 deletions modules/bigbio/onsite/main.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
process ONSITE {
tag "${meta.id}"
tag "${meta.mzml_id}"
label 'process_medium'
label 'onsite'

Expand All @@ -20,7 +20,7 @@ process ONSITE {

script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.mzml_id}"

// Algorithm selection: lucxor (default), ascore, or phosphors
def algorithm = params.onsite_algorithm ?: 'lucxor'
Expand All @@ -42,7 +42,7 @@ process ONSITE {

if (algorithm == 'ascore') {
// AScore: uses -in, -id, -out, --fragment-mass-unit
fragment_unit = params.onsite_fragment_unit ?: 'Da'
fragment_unit = params.onsite_fragment_error_units ?: 'Da'
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
onsite ascore \\
Expand All @@ -55,7 +55,7 @@ process ONSITE {
}
else if (algorithm == 'phosphors') {
// PhosphoRS: uses -in, -id, -out, --fragment-mass-unit
fragment_unit = params.onsite_fragment_unit ?: 'Da'
fragment_unit = params.onsite_fragment_error_units ?: 'Da'
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
onsite phosphors \\
Expand All @@ -82,10 +82,10 @@ process ONSITE {
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)'"
def neutral_losses = params.onsite_neutral_losses ? "--neutral-losses ${params.onsite_neutral_losses}" : "--neutral-losses 'sty -H3PO4 -97.97690'"
def target_mods = params.onsite_target_modifications ? "--target-modifications '${params.onsite_target_modifications}'" : "--target-modifications 'Phospho(S),Phospho(T),Phospho(Y),PhosphoDecoy(A)'"
def neutral_losses = params.onsite_neutral_losses ? "--neutral-losses '${params.onsite_neutral_losses}'" : "--neutral-losses 'sty -H3PO4 -97.97690'"
def decoy_mass = params.onsite_decoy_mass ? "--decoy-mass ${params.onsite_decoy_mass}" : "--decoy-mass 79.966331"
def decoy_losses = params.onsite_decoy_neutral_losses ? "--decoy-neutral-losses ${params.onsite_decoy_neutral_losses}" : "--decoy-neutral-losses 'X -H3PO4 -97.97690'"
def decoy_losses = params.onsite_decoy_neutral_losses ? "--decoy-neutral-losses '${params.onsite_decoy_neutral_losses}'" : "--decoy-neutral-losses 'X -H3PO4 -97.97690'"

def optional_flags = [disable_split_by_charge, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
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