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

Update main.nf #41

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63a9219
Update main.nf
daichengxin Jun 14, 2026
8242ec6
Update main.nf
daichengxin Jun 14, 2026
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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'"
Comment on lines +85 to +88

@coderabbitai coderabbitai Bot Jun 14, 2026

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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Shell injection vulnerability: unescaped single quotes in user-supplied parameters.

Wrapping user-supplied values in single quotes does not prevent shell injection if the value itself contains a single quote. An attacker could break out of the quoting context.

Example: If params.onsite_target_modifications = "Phospho(S)'; rm -rf /; echo '", the resulting command becomes:

--target-modifications 'Phospho(S)'; rm -rf /; echo ''

Escape embedded single quotes before interpolation:

🛡️ Proposed fix: escape single quotes in user values 
         // 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_val = params.onsite_target_modifications ? params.onsite_target_modifications.toString().replaceAll(/'/, "'\"'\"'") : "Phospho(S),Phospho(T),Phospho(Y),PhosphoDecoy(A)"
+        def target_mods = "--target-modifications '${target_mods_val}'"
+        def neutral_losses_val = params.onsite_neutral_losses ? params.onsite_neutral_losses.toString().replaceAll(/'/, "'\"'\"'") : "sty -H3PO4 -97.97690"
+        def neutral_losses = "--neutral-losses '${neutral_losses_val}'"
         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_val = params.onsite_decoy_neutral_losses ? params.onsite_decoy_neutral_losses.toString().replaceAll(/'/, "'\"'\"'") : "X -H3PO4 -97.97690"
+        def decoy_losses = "--decoy-neutral-losses '${decoy_losses_val}'"

The pattern '\"'\"' ends the single-quoted string, appends a double-quoted single quote, then resumes single quoting—a standard shell idiom for embedding literal single quotes.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@modules/bigbio/onsite/main.nf` around lines 85 - 88, The shell command
construction is vulnerable to injection because user-supplied parameters wrapped
in single quotes are not escaped—an attacker could inject a single quote to
break out of the quoting context. Escape embedded single quotes in each
user-supplied parameter before interpolation for the variables target_mods,
neutral_losses, decoy_mass, and decoy_losses. Apply the standard shell idiom
pattern to each `params.onsite_*` reference to convert any embedded single
quotes into a safe format that terminates the quoted string, appends an escaped
quote, and resumes quoting, ensuring that malicious input cannot break the
command structure.


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