fixed

daichengxin · Aug 15, 2024 · 3cccdc2 · 3cccdc2
1 parent 2efeed3
commit 3cccdc2
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
@@ -8,7 +8,7 @@ process SPECTRUM2FEATURES {
         'biocontainers/quantms-utils:0.0.7--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(ms_file), path(id_file)
+    tuple val(meta), path(id_file), path(ms_file)
 
     output:
     tuple val(meta), path("${id_file.baseName}_snr.idXML"), emit: id_files_snr
@@ -20,7 +20,7 @@ process SPECTRUM2FEATURES {
     def prefix = task.ext.prefix ?: "${meta.mzml_id}"
 
     """
-    quantmsutilsc spectrum2feature --ms_path "${ms_path}" --idxml "${id_file}" --output "${id_file.baseName}_snr.idXML" 2>&1 | tee add_snr_feature.log
+    quantmsutilsc spectrum2feature --ms_path "${ms_file}" --idxml "${id_file}" --output "${id_file.baseName}_snr.idXML" 2>&1 | tee add_snr_feature.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/subworkflows/local/psmrescoring.nf b/subworkflows/local/psmrescoring.nf
@@ -11,6 +11,7 @@ include { GETSAMPLE                      } from '../../modules/local/extract_sam
 include { SAGEFEATURE                    } from '../../modules/local/add_sage_feat/main'
 include { IDMERGER                       } from '../../modules/local/openms/idmerger/main'
 include { IDRIPPER                       } from '../../modules/local/openms/idripper/main'
+include { SPECTRUM2FEATURES              } from '../../modules/local/spectrum2features/main'
 
 workflow PSMRESCORING {
     take:
@@ -52,6 +53,13 @@ workflow PSMRESCORING {
             ch_software_versions = ch_software_versions.mix(EXTRACTPSMFEATURES.out.version)
         }
 
+        // Add SNR features to percolator
+        if (params.add_snr_feature_percolator) {
+            SPECTRUM2FEATURES(ch_id_files_feats.combine(ch_file_preparation_results, by: 0))
+            ch_id_files_feats = SPECTRUM2FEATURES.out.id_files_snr
+            ch_software_versions = ch_software_versions.mix(SPECTRUM2FEATURES.out.version)
+        }
+
         // Rescoring for independent run, Sample or whole experiments
         if (params.rescore_range == "independent_run") {
             PERCOLATOR(ch_id_files_feats)