Merge pull request #306 from daichengxin/dev

Add warning info and set mass accurancy automatic for DIA when Dalton input(Don't merge)
bigbio · Oct 18, 2023 · 00c1251 · 00c1251
2 parents 490a547 + 0202115
commit 00c1251
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Showing 5 changed files with 31 additions and 12 deletions.
diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf
@@ -23,13 +23,13 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
 
     script:
     def args = task.ext.args ?: ''
-    mass_acc_ms1 = meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') ? meta['precursormasstolerance'] : 5
-    mass_acc_ms2 = meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm') ? meta['fragmentmasstolerance'] : 13
 
     if (params.mass_acc_automatic) {
-        mass_acc = "--quick-mass-acc --individual-mass-acc"
+        mass_acc = '--quick-mass-acc --individual-mass-acc'
+    } else if (meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') && meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm')){
+        mass_acc = "--mass-acc ${meta['fragmentmasstolerance']} --mass-acc-ms1 ${meta['precursormasstolerance']}"
     } else {
-        mass_acc = "--mass-acc $mass_acc_ms2 --mass-acc-ms1 $mass_acc_ms1"
+        mass_acc = '--quick-mass-acc --individual-mass-acc'
     }
     scan_window = params.scan_window_automatic ? '--individual-windows' : "--window $params.scan_window"
 

diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf
@@ -22,14 +22,15 @@ process DIANN_PRELIMINARY_ANALYSIS {
 
     // I am using here the ["key"] syntax, since the preprocessed meta makes
     // was evaluating to null when using the dot notation.
-    mass_acc_ms1 = meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') ? meta['precursormasstolerance'] : 5
-    mass_acc_ms2 = meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm') ? meta['fragmentmasstolerance'] : 13
 
     if (params.mass_acc_automatic) {
         mass_acc = '--quick-mass-acc --individual-mass-acc'
+    } else if (meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') && meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm')){
+        mass_acc = "--mass-acc ${meta['fragmentmasstolerance']} --mass-acc-ms1 ${meta['precursormasstolerance']}"
     } else {
-        mass_acc = "--mass-acc $mass_acc_ms2 --mass-acc-ms1 $mass_acc_ms1"
+        mass_acc = '--quick-mass-acc --individual-mass-acc'
     }
+
     scan_window = params.scan_window_automatic ? '--individual-windows' : '--window $params.scan_window'
     time_corr_only = params.time_corr_only ? '--time-corr-only' : ''
 

diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf
@@ -31,10 +31,15 @@ process DIANNSUMMARY {
 
     script:
     def args = task.ext.args ?: ''
-    mass_acc_ms1 = meta["precursormasstoleranceunit"].toLowerCase().endsWith("ppm") ? meta["precursormasstolerance"] : 5
-    mass_acc_ms2 = meta["fragmentmasstoleranceunit"].toLowerCase().endsWith("ppm") ? meta["fragmentmasstolerance"] : 13
 
-    mass_acc = params.mass_acc_automatic ? "--quick-mass-acc --individual-mass-acc" : "--mass-acc $mass_acc_ms2 --mass-acc-ms1 $mass_acc_ms1"
+    if (params.mass_acc_automatic) {
+        mass_acc = '--quick-mass-acc --individual-mass-acc'
+    } else if (meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') && meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm')){
+        mass_acc = "--mass-acc ${meta['fragmentmasstolerance']} --mass-acc-ms1 ${meta['precursormasstolerance']}"
+    } else {
+        mass_acc = '--quick-mass-acc --individual-mass-acc'
+    }
+
     scan_window = params.scan_window_automatic ? "--individual-windows" : "--window $params.scan_window"
     species_genes = params.species_genes ? "--species-genes": ""
 

diff --git a/modules/local/individual_final_analysis/main.nf b/modules/local/individual_final_analysis/main.nf
@@ -19,14 +19,19 @@ process INDIVIDUAL_FINAL_ANALYSIS {
 
     script:
     def args = task.ext.args ?: ''
-    mass_acc_ms1 = meta["precursormasstoleranceunit"].toLowerCase().endsWith("ppm") ? meta["precursormasstolerance"] : 5
-    mass_acc_ms2 = meta["fragmentmasstoleranceunit"].toLowerCase().endsWith("ppm") ? meta["fragmentmasstolerance"] : 13
     scan_window = params.scan_window
 
     if (params.mass_acc_automatic | params.scan_window_automatic){
         mass_acc_ms2 = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 11 | tr -cd \"[0-9]\")"
         scan_window = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 19 | tr -cd \"[0-9]\")"
         mass_acc_ms1 = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 15 | tr -cd \"[0-9]\")"
+    } else if (meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') && meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm')){
+        mass_acc_ms1 = meta["precursormasstolerance"]
+        mass_acc_ms2 = meta["fragmentmasstolerance"]
+    } else {
+        mass_acc_ms2 = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 11 | tr -cd \"[0-9]\")"
+        scan_window = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 19 | tr -cd \"[0-9]\")"
+        mass_acc_ms1 = "\$(cat ${diann_log} | grep \"Averaged recommended settings\" | cut -d ' ' -f 15 | tr -cd \"[0-9]\")"
     }
 
     """

diff --git a/workflows/dia.nf b/workflows/dia.nf
@@ -49,6 +49,14 @@ workflow DIA {
 
     meta = ch_result.meta.unique { it[0] }
 
+    if (!params.mass_acc_automatic)
+    {
+        if (meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('da') || meta['precursormasstoleranceunit'].toLowerCase().endsWith('da'))
+        {
+            log.info "Warning: DIA-NN only supports ppm unit tolerance for MS1 and MS2. Falling back to `mass_acc_automatic`=`true` to automatically determine the tolerance by DIA-NN!"
+        }
+    }
+
     DIANNCFG(meta)
     ch_software_versions = ch_software_versions.mix(DIANNCFG.out.version.ifEmpty(null))