Merge pull request #307 from daichengxin/dev

fixed errors
bigbio · Oct 18, 2023 · 4163570 · 4163570
2 parents 00c1251 + 4e895b4
commit 4163570
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Showing 2 changed files with 3 additions and 9 deletions.
diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf
@@ -28,10 +28,12 @@ process DIANN_PRELIMINARY_ANALYSIS {
     } else if (meta['precursormasstoleranceunit'].toLowerCase().endsWith('ppm') && meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('ppm')){
         mass_acc = "--mass-acc ${meta['fragmentmasstolerance']} --mass-acc-ms1 ${meta['precursormasstolerance']}"
     } else {
+        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!"
         mass_acc = '--quick-mass-acc --individual-mass-acc'
     }
 
-    scan_window = params.scan_window_automatic ? '--individual-windows' : '--window $params.scan_window'
+    // Notes: Use double quotes for params, so that it is escaped in the shell.
+    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/workflows/dia.nf b/workflows/dia.nf
@@ -49,14 +49,6 @@ 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))