Merge pull request #25 from biosustain/updt_onsite

ypriverol · web-flow · commit a5ee268891c8 · 2026-03-14T12:28:39.000Z
Updt onsite
diff --git 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/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
@@ -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'
@@ -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 : ''}
         """
-    } 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'
@@ -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} \\
@@ -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")
         algorithm: ${algorithm}
     END_VERSIONS
     """
diff --git 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 +19,51 @@ 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"
diff --git 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") {

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-name: onsite`
`2`	`1`	`channels:`
`3`	`2`	`- conda-forge`
`4`	`3`	`- bioconda`