bump onsite version

modules/bigbio/onsite/environment.yml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::pyonsite=0.0.4
+  - bioconda::pyonsite=0.0.5

modules/bigbio/onsite/main.nf

@@ -4,14 +4,14 @@ process ONSITE {
     label 'onsite'
 
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'oras://ghcr.io/bigbio/pyonsite-sif:0.0.4'
-        : 'ghcr.io/bigbio/pyonsite:0.0.4'}"
+        ? 'oras://ghcr.io/bigbio/pyonsite-sif:0.0.5'
+        : 'ghcr.io/bigbio/pyonsite:0.0.5'}"
 
     input:
     tuple val(meta), path(mzml_file), path(id_file)
 
     output:
-    tuple val(meta), path("${prefix}_*.idparquet"), emit: ptm_in_id_onsite
+    tuple val(meta), path("${prefix}_*.{idparquet,idXML,mzIdentML}"), emit: ptm_in_id_onsite
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -36,6 +36,12 @@ process ONSITE {
     def fragment_unit = ''
     def add_decoys = onsite_add_decoys ? '--add-decoys' : ''
     def debug = params.onsite_debug ? '--debug' : ''
+    def suffix = id_file.name.endsWith(".idparquet")
+        ? "idparquet"
+        : id_file.name.endsWith(".idXML")
+            ? "idXML"
+            : id_file.name.endsWith(".mzIdentML")
+                ? "mzIdentML" : "idparquet"
 
     // Build algorithm-specific command
     def algorithm_cmd = ''
@@ -48,7 +54,7 @@ process ONSITE {
         onsite ascore \\
             -in ${mzml_file} \\
             -id ${id_file} \\
-            -out ${prefix}_ascore.idparquet \\
+            -out ${prefix}_ascore.${suffix} \\
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n            ' + optional_flags : ''}
         """
@@ -61,7 +67,7 @@ process ONSITE {
         onsite phosphors \\
             -in ${mzml_file} \\
             -id ${id_file} \\
-            -out ${prefix}_phosphors.idparquet \\
+            -out ${prefix}_phosphors.${suffix} \\
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit}${optional_flags ? ' \\\n            ' + optional_flags : ''}
             ${args}
@@ -92,7 +98,7 @@ process ONSITE {
         onsite lucxor \\
             -in ${mzml_file} \\
             -id ${id_file} \\
-            -out ${prefix}_lucxor.idparquet \\
+            -out ${prefix}_lucxor.${suffix} \\
             --fragment-method ${fragment_method} \\
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-error-units ${fragment_unit} \\

modules/bigbio/onsite/meta.yml

@@ -35,8 +35,8 @@ input:
         ontologies: []
     - id_file:
         type: file
-        description: Protein/peptide identifications file in idparquet format
-        pattern: "*.idparquet"
+        description: Protein/peptide identifications file
+        pattern: "*.{idparquet,idXML,mzIdentML}"
         ontologies: []
 output:
   ptm_in_id_onsite:
@@ -46,9 +46,9 @@ output:
             Groovy Map containing sample information
       - ${prefix}_*.idparquet:
           type: file
-          description: Output idparquet file containing PTM localization results from
+          description: Output id file containing PTM localization results from
             onsite
-          pattern: "${prefix}_*.idparquet"
+          pattern: "${prefix}_*.{idparquet,idXML,mzIdentML}"
           ontologies: []
   log:
     - "*.log":

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

@@ -90,6 +90,87 @@ nextflow_process {
         }
     }
 
+    test("Should run AScore algorithm with idXML input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['idxml_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_idxml")
+            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 with idXML input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['idxml_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_idxml")
+            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 with idXML input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', mzml_id: 'test_sample' ],
+                    file(params.test_data['proteomics']['onsite']['idxml_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_idxml")
+            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"

tests/config/test_data.config

@@ -22,6 +22,8 @@ params {
                 // Test data for onsite PTM localization module
                 mzml = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/Phospho_redissolve_final_01.mzML"
                 idparquet = System.getenv('ONSITE_IDPARQUET_PATH') ?: "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/Phospho_redissolve_final_01_clean_perc.idparquet"
+                idxml = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/1_consensus_fdr_filter_pep.idXML"
+                idxml_mzml = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/1.mzML"
             }
             qpx {
                 // DIA-NN results for QPX export testing (reuses pmultiqc DIANN example)