using the bigbio onsite module

conf/dev.config

@@ -24,6 +24,6 @@ process {
 
     // ONSITE uses its own container (not OpenMS thirdparty)
     withName: '.*:PHOSPHO_SCORING:ONSITE' {
-        container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pyonsite:0.0.1--pyhdfd78af_0' : 'quay.io/biocontainers/pyonsite:0.0.1--pyhdfd78af_0' }"}
+        container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !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' }"}
     }
 }

modules.json

@@ -40,6 +40,11 @@
         "https://github.com/bigbio/nf-modules.git": {
             "modules": {
                 "bigbio": {
+                    "onsite": {
+                        "branch": "main",
+                        "git_sha": "e4f16df2acb2c084a5043840212d0fb52f69fbbc",
+                        "installed_by": ["modules"]
+                    },
                     "thermorawfileparser": {
                         "branch": "main",
                         "git_sha": "a1a4a11ff508b2b5c23c9fb21c51c3327b748d4d",

modules/bigbio/onsite/environment.yml

@@ -0,0 +1,7 @@
+name: onsite
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::pyonsite=0.0.2

modules/bigbio/onsite/main.nf

@@ -0,0 +1,126 @@
+process ONSITE {
+    tag "$meta.mzml_id"
+    label 'process_medium'
+    label 'onsite'
+
+    container "${ 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' }"
+
+    input:
+    tuple val(meta), path(mzml_file), path(id_file)
+
+    output:
+    tuple val(meta), path("${id_file.baseName}_*.idXML"), emit: ptm_in_id_onsite
+    path "versions.yml", emit: versions
+    path "*.log", emit: log
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
+
+    // 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
+
+    // Algorithm-specific parameters
+    def fragment_unit = ''
+    def add_decoys = onsite_add_decoys ? '--add-decoys' : ''
+    def debug = params.onsite_debug ? '--debug' : ''
+
+    // Build algorithm-specific command
+    def algorithm_cmd = ''
+
+    if (algorithm == 'ascore') {
+        // AScore: uses -in, -id, -out, --fragment-mass-unit
+        fragment_unit = params.onsite_fragment_unit ?: 'Da'
+        algorithm_cmd = """
+        onsite ascore \\
+            -in ${mzml_file} \\
+            -id ${id_file} \\
+            -out ${id_file.baseName}_ascore.idXML \\
+            --fragment-mass-tolerance ${fragment_tolerance} \\
+            --fragment-mass-unit ${fragment_unit} \\
+            ${add_decoys} \\
+            ${compute_all_scores} \\
+            ${debug}
+        """
+    } else if (algorithm == 'phosphors') {
+        // PhosphoRS: uses -in, -id, -out, --fragment-mass-unit
+        fragment_unit = params.onsite_fragment_unit ?: 'Da'
+        algorithm_cmd = """
+        onsite phosphors \\
+            -in ${mzml_file} \\
+            -id ${id_file} \\
+            -out ${id_file.baseName}_phosphors.idXML \\
+            --fragment-mass-tolerance ${fragment_tolerance} \\
+            --fragment-mass-unit ${fragment_unit} \\
+            ${add_decoys} \\
+            ${compute_all_scores} \\
+            ${debug}
+        """
+    } 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'
+        def min_mz = params.onsite_min_mz ?: '150.0'
+        def max_charge = params.onsite_max_charge_state ?: '5'
+        def max_peptide_len = params.onsite_max_peptide_length ?: '40'
+        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 ?: '5'
+        def rt_tolerance = params.onsite_rt_tolerance ?: '0.01'
+        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 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'"
+
+        algorithm_cmd = """
+        onsite lucxor \\
+            -in ${mzml_file} \\
+            -id ${id_file} \\
+            -out ${id_file.baseName}_lucxor.idXML \\
+            --fragment-method ${fragment_method} \\
+            --fragment-mass-tolerance ${fragment_tolerance} \\
+            --fragment-error-units ${fragment_unit} \\
+            --min-mz ${min_mz} \\
+            ${target_mods} \\
+            ${neutral_losses} \\
+            ${decoy_mass} \\
+            ${decoy_losses} \\
+            --max-charge-state ${max_charge} \\
+            --max-peptide-length ${max_peptide_len} \\
+            --max-num-perm ${max_num_perm} \\
+            --modeling-score-threshold ${modeling_threshold} \\
+            --scoring-threshold ${scoring_threshold} \\
+            --min-num-psms-model ${min_num_psms} \\
+            --rt-tolerance ${rt_tolerance} \\
+            ${disable_split_by_charge} \\
+            ${compute_all_scores} \\
+            ${debug}
+        """
+    } else {
+        error "Unknown onsite algorithm: ${algorithm}. Supported algorithms: ascore, phosphors, lucxor"
+    }
+
+    """
+    ${algorithm_cmd} \\
+        2>&1 | tee ${id_file.baseName}_${algorithm}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        onsite: \$(onsite --version 2>&1 | grep -oP 'version \\K[0-9.]+' || echo "unknown")
+        algorithm: ${algorithm}
+    END_VERSIONS
+    """
+}

modules/bigbio/onsite/meta.yml

@@ -0,0 +1,56 @@
+name: onsite
+description: Post-translational modification (PTM) localization using onsite algorithms (AScore, PhosphoRS, LucXor)
+keywords:
+  - onsite
+  - PTM
+  - phosphorylation
+  - AScore
+  - PhosphoRS
+  - LucXor
+  - modification
+  - localization
+tools:
+  - onsite:
+      description: |
+        Comprehensive Python package for mass spectrometry post-translational modification (PTM) localization.
+        Provides algorithms for confident phosphorylation site localization and scoring, including
+        implementations of AScore, PhosphoRS, and LucXor (LuciPHOr2).
+      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"]
+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' ]
+  - 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"
+authors:
+  - "@ypriverol"
+  - "@weizhongchun"

modules/bigbio/onsite/tests/main.nf.test

@@ -0,0 +1,112 @@
+nextflow_process {
+
+    name "Test Process ONSITE"
+    script "../main.nf"
+    process "ONSITE"
+    tag "modules"
+    tag "modules_onsite"
+    tag "onsite"
+
+    test("Should run AScore algorithm") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['mzml'], checkIfExists: true),
+                    file(params.test_data['proteomics']['onsite']['idxml'], checkIfExists: true)
+                ]
+                """
+            }
+            params {
+                onsite_algorithm = 'ascore'
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions_ascore")
+            assert process.out.ptm_in_id_onsite.size() == 1
+            assert process.out.log.size() == 1
+            // Check output file has correct naming
+            assert process.out.ptm_in_id_onsite[0][1].toString().endsWith('_ascore.idXML')
+        }
+    }
+
+    test("Should run PhosphoRS algorithm") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['mzml'], checkIfExists: true),
+                    file(params.test_data['proteomics']['onsite']['idxml'], checkIfExists: true)
+                ]
+                """
+            }
+            params {
+                onsite_algorithm = 'phosphors'
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions_phosphors")
+            assert process.out.ptm_in_id_onsite.size() == 1
+            assert process.out.log.size() == 1
+            // Check output file has correct naming
+            assert process.out.ptm_in_id_onsite[0][1].toString().endsWith('_phosphors.idXML')
+        }
+    }
+
+    test("Should run LucXor algorithm") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['mzml'], checkIfExists: true),
+                    file(params.test_data['proteomics']['onsite']['idxml'], checkIfExists: true)
+                ]
+                """
+            }
+            params {
+                onsite_algorithm = 'lucxor'
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions_lucxor")
+            assert process.out.ptm_in_id_onsite.size() == 1
+            assert process.out.log.size() == 1
+            // Check output file has correct naming
+            assert process.out.ptm_in_id_onsite[0][1].toString().endsWith('_lucxor.idXML')
+        }
+    }
+
+    test("Should run stub mode") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['mzml'], checkIfExists: true),
+                    file(params.test_data['proteomics']['onsite']['idxml'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match("versions_stub")
+        }
+    }
+}

modules/bigbio/onsite/tests/nextflow.config

@@ -0,0 +1,3 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+}