From c02f1698d66dc688a807f6e2452b519159cae172 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 14:00:22 +0100
Subject: [PATCH 1/7] :art: fix linting for onsite (still w/o strict syntax)

---
 modules/bigbio/onsite/environment.yml |  1 -
 modules/bigbio/onsite/main.nf         |  6 ++-
 modules/bigbio/onsite/meta.yml        | 77 +++++++++++++++------------
 3 files changed, 49 insertions(+), 35 deletions(-)

diff --git a/modules/bigbio/onsite/environment.yml b/modules/bigbio/onsite/environment.yml
index f1d5c78..0025aa1 100644
--- a/modules/bigbio/onsite/environment.yml
+++ b/modules/bigbio/onsite/environment.yml
@@ -1,4 +1,3 @@
-name: onsite
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index 4101b3e..67d2e09 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -5,7 +5,7 @@ process 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' }"
+        'biocontainers/pyonsite:0.0.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(mzml_file), path(id_file)
@@ -15,6 +15,9 @@ process 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}"
@@ -60,6 +63,7 @@ process ONSITE {
             -out ${id_file.baseName}_phosphors.idXML \\
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n            ' + optional_flags : ''}
+            ${args}
         """
     } else if (algorithm == 'lucxor') {
         // LucXor: uses -in, -id, -out, --fragment-error-units (note: error-units not mass-unit)
diff --git a/modules/bigbio/onsite/meta.yml b/modules/bigbio/onsite/meta.yml
index 62a06aa..0d19d71 100644
--- a/modules/bigbio/onsite/meta.yml
+++ b/modules/bigbio/onsite/meta.yml
@@ -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
@@ -18,40 +19,50 @@ 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
+      - ${id_file.baseName}_*.idXML:
+          type: file
+          description: idXML file containing PTM localization results from onsite
+          pattern: "${id_file.baseName}_*.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"

From 66baee71ec465fe2409da540db940ecc1e5eb51f Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 14:01:39 +0100
Subject: [PATCH 2/7] :art: add missing tag and exclude test outputs from git

---
 .gitignore                               | 2 ++
 modules/bigbio/onsite/tests/main.nf.test | 1 +
 2 files changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 04c2d80..ea0ae1b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -198,6 +198,8 @@ dag.svg
 testing/
 testing*/
 *.pyc
+.nf-test
+*nf.test.snap
 
 # Codacy
 .codacy
diff --git a/modules/bigbio/onsite/tests/main.nf.test b/modules/bigbio/onsite/tests/main.nf.test
index 8e45206..8caec60 100644
--- a/modules/bigbio/onsite/tests/main.nf.test
+++ b/modules/bigbio/onsite/tests/main.nf.test
@@ -5,6 +5,7 @@ nextflow_process {
     process "ONSITE"
     tag "modules"
     tag "modules_onsite"
+    tag "modules_bigbio"
     tag "onsite"
 
     test("Should run AScore algorithm") {

From 42cd4bccf2a427bfe09280d3e3dcc570e9c8c766 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 15:43:54 +0100
Subject: [PATCH 3/7] Updt onsite prefix (#2)

* Replaced ".mzml_id" to ".id"

* Updated output labels with "prefix"

* Updated output to "prefix"

---------

Co-authored-by: edircoli <edirvidalcastro@gmail.com>
---
 modules/bigbio/onsite/main.nf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index 67d2e09..2f73eb8 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -1,5 +1,5 @@
 process ONSITE {
-    tag "$meta.mzml_id"
+    tag "$meta.id"
     label 'process_medium'
     label 'onsite'
 
@@ -11,7 +11,7 @@ process ONSITE {
     tuple val(meta), path(mzml_file), path(id_file)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_*.idXML"), emit: ptm_in_id_onsite
+    tuple val(meta), path("${task.ext.prefix ?: meta.id}_*.idXML"), emit: ptm_in_id_onsite
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -20,7 +20,7 @@ process ONSITE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     // Algorithm selection: lucxor (default), ascore, or phosphors
     def algorithm = params.onsite_algorithm ?: 'lucxor'
@@ -48,7 +48,7 @@ process ONSITE {
         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 : ''}
         """
@@ -60,7 +60,7 @@ process ONSITE {
         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}
@@ -90,7 +90,7 @@ process ONSITE {
         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} \\
@@ -112,11 +112,11 @@ process ONSITE {
     }
 
     """
-    ${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")
         algorithm: ${algorithm}
     END_VERSIONS
     """

From a62b51ea6de55bb26e381b819e3ffd29cbe5c30f Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 15:45:16 +0100
Subject: [PATCH 4/7] :art: make it compatible to the strict syntax

---
 modules/bigbio/onsite/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index 2f73eb8..d040125 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -43,7 +43,7 @@ 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 {it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite ascore \\
             -in ${mzml_file} \\
@@ -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'
-        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { it }.join(' \\\n            ')
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll {it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite phosphors \\
             -in ${mzml_file} \\
@@ -85,7 +85,7 @@ 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 {it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite lucxor \\
             -in ${mzml_file} \\

From 8da69e3006d94f508f7d1f2b529b457c0bde18f5 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 15:55:07 +0100
Subject: [PATCH 5/7] :art: format document

---
 modules/bigbio/onsite/main.nf | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index d040125..dabf5a0 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -1,11 +1,11 @@
 process ONSITE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
     label 'onsite'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pyonsite:0.0.2--pyhdfd78af_0' :
-        'biocontainers/pyonsite:0.0.2--pyhdfd78af_0' }"
+    container "${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)
@@ -43,7 +43,7 @@ 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 -> it }.join(' \\\n            ')
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite ascore \\
             -in ${mzml_file} \\
@@ -52,10 +52,11 @@ process ONSITE {
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n            ' + optional_flags : ''}
         """
-    } 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 -> it }.join(' \\\n            ')
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite phosphors \\
             -in ${mzml_file} \\
@@ -65,7 +66,8 @@ process ONSITE {
             --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'
@@ -85,7 +87,7 @@ 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 -> it }.join(' \\\n            ')
+        def optional_flags = [disable_split_by_charge, compute_all_scores, debug].findAll { it -> it }.join(' \\\n            ')
         algorithm_cmd = """
         onsite lucxor \\
             -in ${mzml_file} \\
@@ -107,8 +109,9 @@ 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")
     }
 
     """

From 94d800b7c3478c13dd3538f8efd0311d37aab168 Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 16:51:28 +0100
Subject: [PATCH 6/7] :bug: argument name it is not allowed

- it is implicit, so any other name works (somehow)
---
 modules/bigbio/onsite/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index dabf5a0..8a90d7e 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -43,7 +43,7 @@ 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 -> it }.join(' \\\n            ')
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n            ')
         algorithm_cmd = """
         onsite ascore \\
             -in ${mzml_file} \\
@@ -56,7 +56,7 @@ process ONSITE {
     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 -> it }.join(' \\\n            ')
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n            ')
         algorithm_cmd = """
         onsite phosphors \\
             -in ${mzml_file} \\
@@ -87,7 +87,7 @@ 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 -> 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} \\

From eef2a9f42297c9f82d09d219b81df96e57b4e55e Mon Sep 17 00:00:00 2001
From: Henry Webel <heweb@dtu.dk>
Date: Wed, 11 Mar 2026 22:01:24 +0100
Subject: [PATCH 7/7] :art: make prefix global to module

- variable local to script: use def
- variablel global to module: leave out def

Should probably only be done with prefix to not clutter
namespaces. As a global variable prefix is used before it
is defined in the module file.
---
 modules/bigbio/onsite/main.nf  | 4 ++--
 modules/bigbio/onsite/meta.yml | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index 8a90d7e..de82e09 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -11,7 +11,7 @@ process ONSITE {
     tuple val(meta), path(mzml_file), path(id_file)
 
     output:
-    tuple val(meta), path("${task.ext.prefix ?: meta.id}_*.idXML"), emit: ptm_in_id_onsite
+    tuple val(meta), path("${prefix}_*.idXML"), emit: ptm_in_id_onsite
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -20,7 +20,7 @@ process ONSITE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     // Algorithm selection: lucxor (default), ascore, or phosphors
     def algorithm = params.onsite_algorithm ?: 'lucxor'
diff --git a/modules/bigbio/onsite/meta.yml b/modules/bigbio/onsite/meta.yml
index 0d19d71..3956abd 100644
--- a/modules/bigbio/onsite/meta.yml
+++ b/modules/bigbio/onsite/meta.yml
@@ -44,10 +44,11 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-      - ${id_file.baseName}_*.idXML:
+      - ${prefix}_*.idXML:
           type: file
-          description: idXML file containing PTM localization results from onsite
-          pattern: "${id_file.baseName}_*.idXML"
+          description: Output idXML file containing PTM localization results from
+            onsite
+          pattern: "${prefix}_*.idXML"
           ontologies: []
   log:
     - "*.log":