Refactor empirical log parsing logic

modules/local/diann/assemble_empirical_library/main.nf

@@ -19,7 +19,6 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     path "empirical_library.*", emit: empirical_library
     path "assemble_empirical_library.log", emit: log
     path "versions.yml", emit: versions
-    env CALIBRATED_PARAMS_VAL, emit: calibrated_params_val
 
     when:
     task.ext.when == null || task.ext.when
@@ -84,15 +83,6 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
 
     cp report.log.txt assemble_empirical_library.log
 
-    CALIBRATED_PARAMS_VAL="0,0,0"
-    val_mass_acc_ms2=\$(grep "Averaged recommended settings" assemble_empirical_library.log | cut -d ' ' -f 11 | tr -cd "[0-9.]")
-    val_mass_acc_ms1=\$(grep "Averaged recommended settings" assemble_empirical_library.log | cut -d ' ' -f 15 | tr -cd "[0-9.]")
-    val_scan_window=\$(grep "Averaged recommended settings" assemble_empirical_library.log | cut -d ' ' -f 19 | tr -cd "[0-9.]")
-    if [ -z "\$val_mass_acc_ms2" ]; then val_mass_acc_ms2="0"; fi
-    if [ -z "\$val_mass_acc_ms1" ]; then val_mass_acc_ms1="0"; fi
-    if [ -z "\$val_scan_window" ]; then val_scan_window="0"; fi
-    export CALIBRATED_PARAMS_VAL="\${val_mass_acc_ms2},\${val_mass_acc_ms1},\${val_scan_window}"
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")

modules/local/diann/assemble_empirical_library/meta.yml

@@ -35,9 +35,5 @@ output:
       type: file
       description: File containing software version
       pattern: "versions.yml"
-  - calibrated_params_val:
-      type: string
-      description: A comma-separated string containing mass_acc_ms2, mass_acc_ms1, and scan_window extracted from the DIA-NN log.
-      pattern: "*,*,*"
 authors:
   - "@daichengxin"

modules/local/parse_empirical_log_task/main.nf

@@ -0,0 +1,24 @@
+process PARSE_EMPIRICAL_LOG_TASK {
+    label 'process_single'
+
+    input:
+    path log_file
+
+    output:
+    stdout emit: parsed_vals
+
+    script:
+    """
+    val_mass_acc_ms2=\$(grep "Averaged recommended settings" ${log_file} | cut -d ' ' -f 11 | tr -cd "[0-9.]")
+    val_mass_acc_ms1=\$(grep "Averaged recommended settings" ${log_file} | cut -d ' ' -f 15 | tr -cd "[0-9.]")
+    val_scan_window=\$(grep "Averaged recommended settings" ${log_file} | cut -d ' ' -f 19 | tr -cd "[0-9.]")
+
+    if [ -z "\$val_mass_acc_ms2" ]; then val_mass_acc_ms2=${params.mass_acc_ms2}; fi
+    if [ -z "\$val_mass_acc_ms1" ]; then val_mass_acc_ms1=${params.mass_acc_ms1}; fi
+    if [ -z "\$val_scan_window" ]; then val_scan_window=${params.scan_window}; fi
+
+    CALIBRATED_PARAMS_VAL="\${val_mass_acc_ms2},\${val_mass_acc_ms1},\${val_scan_window}"
+
+    echo -n "\$CALIBRATED_PARAMS_VAL"
+    """
+}

modules/local/parse_empirical_log_task/meta.yml

@@ -0,0 +1,26 @@
+name: "parse_empirical_log_task"
+description: "Parses the empirical assembly log file (from DIA-NN) to extract calibrated mass accuracies and scan window parameters for downstream analysis."
+keywords:
+  - quantmsdiann
+  - diann
+  - log
+  - parse
+  - proteomics
+  - mass_accuracy
+tools:
+  - "coreutils":
+      description: "Standard GNU core utilities (grep, cut, tr, echo) used for text processing and log parsing."
+      homepage: "https://www.gnu.org/software/coreutils/"
+      documentation: "https://www.gnu.org/software/coreutils/manual/"
+input:
+  - log_file:
+      type: file
+      description: "The log file generated by the empirical library assembly step (DIA-NN stdout/stderr log) containing the Averaged recommended settings."
+      pattern: "*.log"
+output:
+  - parsed_vals:
+      type: string
+      description: "A comma-separated string containing extracted mass_acc_ms2, mass_acc_ms1, and scan_window values (e.g., '15,20,8')."
+      pattern: "*,*,*"
+authors:
+  - "@bigbio"

subworkflows/local/parse_empirical_log/main.nf

@@ -0,0 +1,16 @@
+
+include { PARSE_EMPIRICAL_LOG_TASK } from '../../../modules/local/parse_empirical_log_task'
+
+workflow PARSE_EMPIRICAL_LOG {
+    take:
+    ch_log_file
+
+    main:
+    PARSE_EMPIRICAL_LOG_TASK(ch_log_file)
+
+    ch_parsed_vals = PARSE_EMPIRICAL_LOG_TASK.out.parsed_vals
+        .ifEmpty("${params.mass_acc_ms2},${params.mass_acc_ms1},${params.scan_window}")
+
+    emit:
+    parsed_vals = ch_parsed_vals
+}

subworkflows/local/parse_empirical_log/meta.yml

@@ -0,0 +1,25 @@
+name: "parse_empirical_log"
+description: "Subworkflow for parsing the empirical assembly log file (from DIA-NN) to extract calibrated parameters."
+keywords:
+  - parse
+  - log
+  - diann
+  - proteomics
+  - parameters
+  - mass_accuracy
+components:
+  - parse_empirical_log_task
+input:
+  - ch_log_file:
+      type: file
+      description: |
+        The log file generated by the empirical library assembly step. Can be an empty channel if the user did not provide a log file.
+output:
+  - parsed_vals:
+      type: string
+      description: |
+        A value channel containing a comma-separated string of the extracted parameters (mass_acc_ms2, mass_acc_ms1, scan_window). Falls back to default pipeline parameters if the log is empty or invalid.
+authors:
+  - "@bigbio"
+maintainers:
+  - "@bigbio"

workflows/dia.nf

@@ -9,7 +9,7 @@
 //
 include { DIANN_MSSTATS               } from '../modules/local/diann/diann_msstats/main'
 include { PRELIMINARY_ANALYSIS        } from '../modules/local/diann/preliminary_analysis/main'
-include { PARSE_EMPIRICAL_LOG         } from '../modules/local/parse_empirical_log/main'
+include { PARSE_EMPIRICAL_LOG         } from '../subworkflows/local/parse_empirical_log/main'
 include { ASSEMBLE_EMPIRICAL_LIBRARY  } from '../modules/local/diann/assemble_empirical_library/main'
 include { INSILICO_LIBRARY_GENERATION } from '../modules/local/diann/insilico_library_generation/main'
 include { INDIVIDUAL_ANALYSIS         } from '../modules/local/diann/individual_analysis/main'
@@ -61,19 +61,12 @@ workflow DIA {
 
     if (params.skip_preliminary_analysis) {
         if (params.empirical_assembly_log) {
-            ch_log_file = Channel.fromPath(params.empirical_assembly_log, checkIfExists: true)
-            PARSE_EMPIRICAL_LOG(ch_log_file)
-            ch_parsed_vals = PARSE_EMPIRICAL_LOG.out.parsed_vals.map { parsed_str ->
-                def clean_str = parsed_str.trim()
-                if (clean_str == "0,0,0") {
-                    return "${params.mass_acc_ms2},${params.mass_acc_ms1},${params.scan_window}"
-                } else {
-                    return clean_str
-                }
-            }
+            ch_empirical_log = Channel.fromPath(params.empirical_assembly_log, checkIfExists: true)
         } else {
-            ch_parsed_vals = Channel.value("${params.mass_acc_ms2},${params.mass_acc_ms1},${params.scan_window}")
+            ch_empirical_log = Channel.empty()
         }
+        PARSE_EMPIRICAL_LOG(ch_empirical_log)
+        ch_parsed_vals = PARSE_EMPIRICAL_LOG.out.parsed_vals
         indiv_fin_analysis_in = ch_file_preparation_results
             .combine(ch_searchdb)
             .combine(speclib)
@@ -123,10 +116,12 @@ workflow DIA {
         )
         ch_software_versions = ch_software_versions
             .mix(ASSEMBLE_EMPIRICAL_LIBRARY.out.versions)
+        PARSE_EMPIRICAL_LOG(ASSEMBLE_EMPIRICAL_LIBRARY.out.log)
+        ch_parsed_vals = PARSE_EMPIRICAL_LOG.out.parsed_vals
         indiv_fin_analysis_in = ch_file_preparation_results
             .combine(ch_searchdb)
             .combine(ASSEMBLE_EMPIRICAL_LIBRARY.out.empirical_library)
-            .combine(ASSEMBLE_EMPIRICAL_LIBRARY.out.calibrated_params_val)
+            .combine(ch_parsed_vals)
             .map { meta_map, ms_file, fasta, library, param_string ->
                 def values = param_string.trim().split(',')
                 def new_meta = meta_map + [