update quantms-rescoring and support AalphaPeptDeep model

conf/modules/modules.config

@@ -216,7 +216,7 @@ process {
     // MS2RESCORE
     withName: 'MSRESCORE_FEATURES' {
         ext.args   = [
-            "--ms2pip_model ${params.ms2pip_model}",
+            "--ms2_model ${params.ms2_model}",
             "--calibration_set_size ${params.calibration_set_size}",
             params.feature_generators.trim() ? "--feature_generators ${params.feature_generators}" : ''
         ].join(' ').trim()

modules/local/utils/msrescore_features/main.nf

@@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.10--pyhdfd78af_0' :
-        'biocontainers/quantms-rescoring:0.0.10--pyhdfd78af_0' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.11' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.11' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
@@ -46,16 +46,23 @@ process MSRESCORE_FEATURES {
         force_model = ""
     }
 
+    if (params.mask_modloss) {
+        mask_modloss = "--mask_modloss"
+    } else {
+        mask_modloss = ""
+    }
+
     """
     rescoring msrescore2feature \\
         --idxml $idxml \\
         --mzml $mzml \\
         --ms2_tolerance $ms2_tolerance \\
         --output ${idxml.baseName}_ms2rescore.idXML \\
-        --ms2pip_model_dir ${params.ms2pip_model_dir} \\
+        --ms2_model_dir ${params.ms2_model_dir} \\
         --processes $task.cpus \\
         --find_best_model \\
         ${force_model} \\
+        ${mask_modloss} \\
         $args \\
         2>&1 | tee ${idxml.baseName}_ms2rescore.log
 

nextflow.config

@@ -111,13 +111,14 @@ params {
 
     // MSRESCORE flags
     ms2rescore                      = false
-    ms2pip_model_dir                = null
+    ms2_model_dir                   = null
     rescore_range                   = 'independent_run'
-    ms2pip_model                    = 'HCD2021'
+    ms2_model                       = 'HCD2021'
     feature_generators              = 'deeplc,ms2pip'
     calibration_set_size            = 0.15
     ms2rescore_fragment_tolerance   = 0.05     // Unit Da
     force_model                     = false
+    mask_modloss                    = true
 
     // SNR features flags
     add_snr_feature_percolator      = false

nextflow_schema.json

@@ -512,15 +512,15 @@
                     "default": "independent_run",
                     "enum": ["independent_run", "by_sample", "by_project"]
                 },
-                "ms2pip_model": {
+                "ms2_model": {
                     "type": "string",
                     "description": "Which deep learning model to generate feature.",
                     "fa_icon": "fas fa-font",
                     "default": "HCD2021"
                 },
-                "ms2pip_model_dir": {
+                "ms2_model_dir": {
                     "type": "string",
-                    "description": "The path of ms2pip model files. Providing model file to avoid repeated download and slow internet connection",
+                    "description": "The path of ms2 prediction model files. Providing model file to avoid repeated download and slow internet connection",
                     "fa_icon": "fas fa-font"
                 },
                 "feature_generators": {
@@ -547,6 +547,12 @@
                     "default": false,
                     "fa_icon": "far fa-check-square"
                 },
+                "mask_modloss": {
+                    "type": "boolean",
+                    "description": "If modloss ions are masked to zeros in the ms2 model. modloss ions are mostly useful for phospho MS2 prediction model.",
+                    "default": true,
+                    "fa_icon": "far fa-check-square"
+                },
                 "run_fdr_cutoff": {
                     "type": "number",
                     "description": "FDR cutoff on PSM level (or peptide level; see Percolator options) *per run* before going into feature finding, map alignment and inference. This can be seen as a pre-filter. See ",