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Merged
ypriverol merged 7 commits into from
Mar 14, 2026
Merged

Updt onsite #25

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c02f169
:art: fix linting for onsite (still w/o strict syntax)
enryH Mar 11, 2026
66baee7
:art: add missing tag and exclude test outputs from git
enryH Mar 11, 2026
42cd4bc
Updt onsite prefix (#2)
enryH Mar 11, 2026
a62b51e
:art: make it compatible to the strict syntax
enryH Mar 11, 2026
8da69e3
:art: format document
enryH Mar 11, 2026
94d800b
:bug: argument name it is not allowed
enryH Mar 11, 2026
eef2a9f
:art: make prefix global to module
enryH Mar 11, 2026
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -198,6 +198,8 @@ dag.svg
testing/
testing*/
*.pyc
.nf-test
*nf.test.snap

# Codacy
.codacy
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1 change: 0 additions & 1 deletion modules/bigbio/onsite/environment.yml
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@@ -1,4 +1,3 @@
name: onsite
channels:
- conda-forge
- bioconda
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43 changes: 25 additions & 18 deletions modules/bigbio/onsite/main.nf
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@@ -1,23 +1,26 @@
process ONSITE {
tag "$meta.mzml_id"
tag "${meta.id}"
label 'process_medium'
label 'onsite'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pyonsite:0.0.2--pyhdfd78af_0' :
'quay.io/biocontainers/pyonsite:0.0.2--pyhdfd78af_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/pyonsite:0.0.2--pyhdfd78af_0'
: 'biocontainers/pyonsite:0.0.2--pyhdfd78af_0'}"

input:
tuple val(meta), path(mzml_file), path(id_file)

output:
tuple val(meta), path("${id_file.baseName}_*.idXML"), emit: ptm_in_id_onsite
tuple val(meta), path("${prefix}_*.idXML"), emit: ptm_in_id_onsite
path "versions.yml", emit: versions
path "*.log", emit: log

when:
task.ext.when == null || task.ext.when

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

// Algorithm selection: lucxor (default), ascore, or phosphors
def algorithm = params.onsite_algorithm ?: 'lucxor'
Expand All @@ -40,28 +43,31 @@ process ONSITE {
if (algorithm == 'ascore') {
// AScore: uses -in, -id, -out, --fragment-mass-unit
fragment_unit = params.onsite_fragment_unit ?: 'Da'
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { it }.join(' \\\n ')
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
onsite ascore \\
-in ${mzml_file} \\
-id ${id_file} \\
-out ${id_file.baseName}_ascore.idXML \\
-out ${prefix}_ascore.idXML \\
--fragment-mass-tolerance ${fragment_tolerance} \\
--fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n ' + optional_flags : ''}
"""
Comment on lines 47 to 54
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@coderabbitai coderabbitai Bot Mar 12, 2026 •
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⚠️ Potential issue | 🟡 Minor

Inconsistent ${args} handling across algorithms.

The phosphors algorithm (line 67) includes ${args} in its command, but ascore (lines 47-54) and lucxor (lines 91-111) do not. This means task.ext.args only affects the phosphors algorithm.

If this is intentional (e.g., only phosphors supports additional arguments), consider adding a comment to clarify. Otherwise, add ${args} consistently to all algorithms.

Proposed fix to add args consistently

For ascore (after line 53):

             --fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n            ' + optional_flags : ''}
+            ${args}

For lucxor (after line 110):

             --rt-tolerance ${rt_tolerance}${optional_flags ? ' \\\n            ' + optional_flags : ''}
+            ${args}
🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@modules/bigbio/onsite/main.nf` around lines 47 - 54, The ascore and lucxor
algorithm command templates (variable algorithm_cmd in the ascore block and the
lucxor block) currently omit ${args} while the phosphors block uses it, causing
task.ext.args to only apply to phosphors; update the ascore and lucxor
algorithm_cmd strings to append ${args} in the same position phosphors does
(preserving optional_flags handling) so task.ext.args is applied consistently,
or alternatively add a clear comment in both the ascore and lucxor blocks
explaining why ${args} is intentionally omitted if that was the intended
behavior.

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@enryH enryH Mar 13, 2026

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@ypriverol should I add it or not?

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@coderabbitai coderabbitai Bot Mar 13, 2026

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Seems like the humans are having a chat. I'll hop back into my burrow for now. If you need me again, just tag @coderabbitai in a new comment, and I'll come hopping out!

} else if (algorithm == 'phosphors') {
}
else if (algorithm == 'phosphors') {
// PhosphoRS: uses -in, -id, -out, --fragment-mass-unit
fragment_unit = params.onsite_fragment_unit ?: 'Da'
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { it }.join(' \\\n ')
def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
onsite phosphors \\
-in ${mzml_file} \\
-id ${id_file} \\
-out ${id_file.baseName}_phosphors.idXML \\
-out ${prefix}_phosphors.idXML \\
--fragment-mass-tolerance ${fragment_tolerance} \\
--fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n ' + optional_flags : ''}
${args}
"""
} else if (algorithm == 'lucxor') {
}
else if (algorithm == 'lucxor') {
// LucXor: uses -in, -id, -out, --fragment-error-units (note: error-units not mass-unit)
fragment_unit = params.onsite_fragment_error_units ?: 'Da'
def fragment_method = params.onsite_fragment_method ?: 'CID'
Expand All @@ -81,12 +87,12 @@ process ONSITE {
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 optional_flags = [disable_split_by_charge, compute_all_scores, debug].findAll { it }.join(' \\\n ')
def optional_flags = [disable_split_by_charge, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')
algorithm_cmd = """
onsite lucxor \\
-in ${mzml_file} \\
-id ${id_file} \\
-out ${id_file.baseName}_lucxor.idXML \\
-out ${prefix}_lucxor.idXML \\
--fragment-method ${fragment_method} \\
--fragment-mass-tolerance ${fragment_tolerance} \\
--fragment-error-units ${fragment_unit} \\
Expand All @@ -103,16 +109,17 @@ process ONSITE {
--min-num-psms-model ${min_num_psms} \\
--rt-tolerance ${rt_tolerance}${optional_flags ? ' \\\n ' + optional_flags : ''}
"""
} else {
error "Unknown onsite algorithm: ${algorithm}. Supported algorithms: ascore, phosphors, lucxor"
}
else {
error("Unknown onsite algorithm: ${algorithm}. Supported algorithms: ascore, phosphors, lucxor")
}

"""
${algorithm_cmd.trim()} 2>&1 | tee ${id_file.baseName}_${algorithm}.log
${algorithm_cmd.trim()} 2>&1 | tee ${prefix}_${algorithm}.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
onsite: \$(onsite --version 2>&1 | grep -oP 'version \\K[0-9.]+' || echo "unknown")
onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")
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⚠️ Potential issue | 🔴 Critical

Bug: \K is a PCRE feature but grep -oE uses ERE.

The \K (reset match start) is a Perl-compatible regex feature that only works with grep -oP. Using it with grep -oE (Extended regex) will fail to extract the version correctly—it will try to match the literal characters \K.

Proposed fix

Either revert to -oP (requires PCRE-enabled grep):

-        onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")
+        onsite: \$(onsite --version 2>&1 | grep -oP 'version \\K[0-9.]+' || echo "unknown")

Or use ERE-compatible approach with sed:

-        onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")
+        onsite: \$(onsite --version 2>&1 | sed -n 's/.*version \\([0-9.]*\\).*/\\1/p' | head -1 || echo "unknown")

Or with awk:

-        onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")
+        onsite: \$(onsite --version 2>&1 | awk '/version/ {for(i=1;i<=NF;i++) if($i ~ /^[0-9.]+$/) {print $i; exit}}' || echo "unknown")
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")
onsite: \$(onsite --version 2>&1 | grep -oP 'version \\K[0-9.]+' || echo "unknown")
🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@modules/bigbio/onsite/main.nf` at line 122, The current extraction in the
onsite version command uses a PCRE-only token (\K) with grep -oE which is ERE
and will not work; update the command in the onsite version assignment to use a
PCRE-enabled grep (change grep -oE to grep -oP) or replace the grep usage with
an ERE-compatible pipeline (e.g., pipe through sed or awk to capture the numeric
version) so that the version is correctly extracted from the output of the
onsite --version invocation.

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@ypriverol ypriverol Mar 13, 2026

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@enryH @jpfeuffer should we accept this suggestion.

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Seems like the humans are having a chat. I'll hop back into my burrow for now. If you need me again, just tag @coderabbitai in a new comment, and I'll come hopping out!

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@enryH enryH Mar 15, 2026

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yes, I would. Did yo add it?

algorithm: ${algorithm}
END_VERSIONS
"""
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78 changes: 45 additions & 33 deletions modules/bigbio/onsite/meta.yml
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@@ -1,5 +1,6 @@
name: onsite
description: Post-translational modification (PTM) localization using onsite algorithms (AScore, PhosphoRS, LucXor)
description: Post-translational modification (PTM) localization using onsite
algorithms (AScore, PhosphoRS, LucXor)
keywords:
- onsite
- PTM
Expand All @@ -18,40 +19,51 @@ tools:
homepage: https://github.com/bigbio/onsite
documentation: https://github.com/bigbio/onsite/blob/main/README.md
tool_dev_url: https://github.com/bigbio/onsite
doi: ""
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', mzml_id:'sample1' ]
- mzml_file:
type: file
description: Input spectrum file in mzML format
pattern: "*.mzML"
- id_file:
type: file
description: Protein/peptide identifications file in idXML format
pattern: "*.idXML"
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'test', mzml_id:'sample1' ]`
- mzml_file:
type: file
description: Input spectrum file in mzML format
pattern: "*.mzML"
ontologies: []
- id_file:
type: file
description: Protein/peptide identifications file in idXML format
pattern: "*.idXML"
ontologies: []
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', mzml_id:'sample1' ]
- ptm_in_id_onsite:
type: file
description: Protein/peptide identifications file with PTM localization scores
pattern: "*_{ascore,phosphors,lucxor}.idXML"
- log:
type: file
description: Log file from onsite execution
pattern: "*.log"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
ptm_in_id_onsite:
- - meta:
type: map
description: |
Groovy Map containing sample information
- ${prefix}_*.idXML:
type: file
description: Output idXML file containing PTM localization results from
onsite
pattern: "${prefix}_*.idXML"
ontologies: []
log:
- "*.log":
type: file
description: Log file from onsite execution
pattern: "*.log"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750
authors:
- "@ypriverol"
- "@weizhongchun"
- "@enryh"
1 change: 1 addition & 0 deletions modules/bigbio/onsite/tests/main.nf.test
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Expand Up @@ -5,6 +5,7 @@ nextflow_process {
process "ONSITE"
tag "modules"
tag "modules_onsite"
tag "modules_bigbio"
tag "onsite"

test("Should run AScore algorithm") {
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