Wang-Bioinformatics-Lab · mwang87 · Jun 20, 2025 · Jun 20, 2025 · Jun 20, 2025 · Jun 20, 2025
diff --git a/bin/NextflowModules b/bin/NextflowModules
diff --git a/nf_workflow.nf b/nf_workflow.nf
@@ -5,13 +5,27 @@ nextflow.enable.dsl=2
 params.input_spectra = "$baseDir/data/"
 
 //This publish dir is mostly  useful when we want to import modules in other workflows, keep it here usually don't change it
-params.publishdir = "$baseDir/nf_output"
+params.publishdir = "$launchDir"
 TOOL_FOLDER = "$moduleDir/bin"
 MODULES_FOLDER = "$TOOL_FOLDER/NextflowModules"
 
-// A lot of useful modules are already implemented and added to the nextflow modules, you can import them to use
-include {summaryLibrary} from "$MODULES_FOLDER/nf_library_search_modules.nf" addParams(publishDir: params.publishdir)
 
+// 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 = "${_publishdir}/nf_output"
+
+// A lot of useful modules are already implemented and added to the nextflow modules, you can import them to use
+// the publishdir is a key word that we're using around all our modules to control where the output files will be saved
+include {summaryLibrary} from "$MODULES_FOLDER/nf_library_search_modules.nf" addParams(publishdir: _publishdir)
 
 process processDataPython {
     /* This is a sample process that runs a python script.
@@ -22,7 +36,7 @@ process processDataPython {
     The script block contains the command that will be run in the process.
     */
 
-    publishDir "$params.publishdir", mode: 'copy'
+    publishDir "$_publishdir", mode: 'copy'
 
     conda "$TOOL_FOLDER/conda_env.yml"
 

diff --git a/workflowinput.yaml b/workflowinput.yaml
@@ -1,7 +1,7 @@
 workflowname: template_nextflow_workflow
 workflowdescription: template_nextflow_workflow
 workflowlongdescription: This is a template nextflow workflow for GNPS2
-workflowversion: "0.1"
+workflowversion: "2025.06.20"
 workflowfile: nf_workflow.nf
 workflowautohide: false
 adminonly: false
+1 −1		bin/GNPS_sharedcode
+5 −0		bin/library_search/conda_env.yml
+942 −0		bin/library_search/gnps_index.py
+473 −0		bin/library_search/library_search_indexed.py
+12 −4		bin/library_search/library_search_wrapper.py
+87 −0		bin/library_search/temp/34f610f3-39a7-35a8-aa4e-0db4017fda8d:__xianghu_tsv_rest.mgf.tsv
+12,779 −0		bin/library_search/test.ipynb
+59 −8		nf_library_search_modules.nf