prepare to use workflow publish

without output {}, nothing is publishded (see nextflow-io/nextflow#5460 ) if output block is defined, nextflow errors out with unclear error. leaving like this for now.
DessimozLab · Dec 18, 2024 · 708fdc7 · 708fdc7
1 parent 6b77e7a
commit 708fdc7
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Showing 3 changed files with 39 additions and 24 deletions.
diff --git a/main.nf b/main.nf
@@ -53,32 +53,44 @@ workflow OMA_browser_build {
         def vps_base = params.pairwise_orthologs_folder
         OMA_BROWSER_BUILD(genomes_dir, matrix_file, hog_orthoxml, vps_base)
 
-    publish:
-        OMA_BROWSER_BUILD.out.db >> "main_db"
-        OMA_BROWSER_BUILD.out.seqidx_h5 >> "data"
+    emit:
+        db = OMA_BROWSER_BUILD.out.db
+        seqidx = OMA_BROWSER_BUILD.out.seqidx_h5
+        downloads = OMA_BROWSER_BUILD.out.downloads
 }
 
-output {
-    'main_db' {
-        path { db ->
-            { file -> "data/OmaServer.h5" }
-        }
-    }
+workflow {
+    main:
+        OMA_browser_build()
+
+    publish:
+        OMA_browser_build.out.db          >> 'main_db'
+        OMA_browser_build.out.seqidx      >> 'data'
+        OMA_browser_build.out.downloads   >> 'downloads'
 
-    'data' { mode 'copy'}
 }
 
-workflow {
-    OMA_browser_build()
-
-    workflow.onComplete {
-        println "Pipeline completed at: ${workflow.complete}"
-        println "Time to complete workflow execution: ${workflow.duration}"
-        println "Execution status: ${workflow.success ? 'Successful' : 'Failed'}"
-        println "Reports stored in ${params.outputDir}/reports/nextflow"
-    }
-
-    workflow.onError {
-        println "Error... Pipeline execution stopped with the following message: $workflow.errorMessage"
-    }
+workflow.onComplete {
+    println "Pipeline completed at: ${workflow.complete}"
+    println "Time to complete workflow execution: ${workflow.duration}"
+    println "Execution status: ${workflow.success ? 'Successful' : 'Failed'}"
+    println "Reports stored in ${params.outputDir}/reports/nextflow"
 }
+
+workflow.onError {
+    println "Error... Pipeline execution stopped with the following message: $workflow.errorMessage"
+}
+
+
+//output {
+//   main_db {
+//       path { db ->
+//           { file -> "data/OmaServer.h5" }
+//       }
+//   }
+//
+//   data      { mode 'copy' }
+//   downloads { mode 'copy' }
+//}
+
+
diff --git a/nextflow.config b/nextflow.config
@@ -2,6 +2,8 @@
 nextflow.enable.moduleBinaries = true // Enables the use of modules with binary scripts
 nextflow.preview.output = true        // Enables publish/output section for workflows
 
+outputDir = "./res-new"
+
 // Global default params
 params {
     // input output parameters

diff --git a/workflows/oma_browser_build.nf b/workflows/oma_browser_build.nf
@@ -39,6 +39,7 @@ workflow OMA_BROWSER_BUILD {
         }
         CACHE_BUILDER(IMPORT_HDF5.out.db_h5)
         GEN_BROWSER_AUX_FILES(IMPORT_HDF5.out.db_h5)
+        download_files = GEN_BROWSER_AUX_FILES.out.genomes_json.mix(GEN_BROWSER_AUX_FILES.out.speciestree)
 
         // create crossreferences
         GENERATE_XREFS(EXTRACT_DARWIN.out.gs_file,
@@ -66,7 +67,7 @@ workflow OMA_BROWSER_BUILD {
     emit:
         db        = COMBINE_HDF.out.combined_h5
         seqidx_h5 = IMPORT_HDF5.out.seqidx_h5
-
+        downloads = download_files
 
 }