updating

Author: mwang87

workflow/workflow.nf

@@ -10,9 +10,23 @@ params.extractnaming = 'condensed' //condensed means it is mangled, original mea
 params.maxfilesize = "3000" // Default 3000 MB
 
 TOOL_FOLDER = "$baseDir/bin"
-params.publishdir = "nf_output"
+params.publishdir = "$launchDir"
 params.PYTHONRUNTIME = "python" // this is a hack because CCMS cluster does not have python installed
 
+
+// COMPATIBILITY NOTE: The following might be necessary if this workflow is being deployed in a slightly different environemnt
+// checking if outdir is defined,
+// if so, then set publishdir to outdir
+if (params.outdir) {
+    _publishdir = params.outdir
+}
+else{
+    _publishdir = params.publishdir
+}
+
+// Augmenting with nf_output
+_publishdir = "${_publishdir}/nf_output"
+
 // This is the parallel run that will run on the cluster
 process queryData {
     errorStrategy 'ignore'
@@ -77,7 +91,7 @@ process queryData2 {
 
 // Merging the results, 100 results at a time, and then doing a full merge
 process formatResultsMergeRounds {
-    publishDir "$params.publishdir/msql", mode: 'copy'
+    publishDir "$_publishdir/msql", mode: 'copy'
     cache false
 
     //errorStrategy 'ignore'
@@ -102,7 +116,7 @@ process formatResultsMergeRounds {
 
 // Merging the JSON in rounds, 100 files at a time
 process formatExtractedSpectraRounds {
-    publishDir "$params.publishdir/extracted", mode: 'copy'
+    publishDir "$_publishdir/extracted", mode: 'copy'
     cache false
     errorStrategy 'ignore'
 
@@ -183,7 +197,7 @@ process formatExtractedSpectraRounds {
 
 
 process summarizeResults {
-    publishDir "$params.publishdir/summary", mode: 'copy'
+    publishDir "$_publishdir/summary", mode: 'copy'
     cache false
     errorStrategy 'ignore'
 
@@ -227,14 +241,14 @@ workflow {
 
     _merged_temp_summary_ch = formatResultsMergeRounds(_query_results_ch.collate( 100 ))
 
-    _query_results_merged_ch = _merged_temp_summary_ch.collectFile(name: "merged_query_results.tsv", storeDir: "$params.publishdir/msql", keepHeader: true)
+    _query_results_merged_ch = _merged_temp_summary_ch.collectFile(name: "merged_query_results.tsv", storeDir: "$_publishdir/msql", keepHeader: true)
 
 
     if(params.extract == "YES"){
         (_, _, _, _extracted_summary_ch) = formatExtractedSpectraRounds(_query_extract_results_ch.collate( 100 ))
 
         // Once we've done this, then we'lll do the actual merge
-        _extracted_summary_ch.collectFile(name: "extracted.tsv", storeDir: "$params.publishdir/extracted", keepHeader: true)
+        _extracted_summary_ch.collectFile(name: "extracted.tsv", storeDir: "$_publishdir/extracted", keepHeader: true)
     }
 
     summarizeResults(_query_results_merged_ch)

workflow/workflowdisplay.yaml

@@ -24,10 +24,10 @@ Views:
                 data: mslevel
             -   title: "query_index"
                 data: query_index
-        columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
-            return `
-            <a target="_blank" href="/dashboards/lcms?usi=mzspec:GNPS2-${task}-${encodeURIComponent(row["filename"])}">None</a>
-            `;}}]'
+        # columnDefs: '[ {"targets": 0,"data": null,"render": function ( data, type, row, meta ) {
+        #     return `
+        #     <a target="_blank" href="/dashboards/lcms?usi=mzspec:GNPS2-${task}-${encodeURIComponent(row["filename"])}">None</a>
+        #     `;}}]'
 
 # TODO: Show the extraction results
 

workflow/workflowinput.yaml

@@ -1,7 +1,7 @@
 workflowname: massql_workflow
 workflowdescription: massql_workflow
 workflowlongdescription: This is a MassQL Workflow
-workflowversion: "2025.08.08"
+workflowversion: "2025.08.15"
 workflowfile: workflow.nf
 workflowautohide: false
 adminonly: false