ensure no-domain works

DessimozLab · Jan 16, 2025 · 77dac24 · 77dac24
1 parent a329a31
commit 77dac24
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Showing 2 changed files with 13 additions and 18 deletions.
diff --git a/subworkflows/local/domains/main.nf b/subworkflows/local/domains/main.nf
@@ -3,17 +3,22 @@
 // Modules
 include {ADD_DOMAINS} from "./../../../modules/local/domains"
 
+def createEmptyFile() {
+    def emptyFile = file("empty.txt")
+    emptyFile.text = "" // Write an empty string
+    return emptyFile
+}
+
 workflow DOMAINS {
     take:
         database
-        known_domains
-        cath_names
-        pfam_names
 
     main:
         // TODO should be extended to include computation of new domain annotation
         // for unknown sequences
-
+        known_domains = (params.known_domains != null) ? Channel.fromPath("${params.known_domains}/*") : Channel.fromPath(createEmptyFile())
+        cath_names = (params.cath_names_path != null) ? Channel.fromPath(params.cath_names_path) : Channel.fromPath(createEmptyFile())
+        pfam_names = (params.pfam_names_path != null) ? Channel.fromPath(params.pfam_names_path) : Channel.fromPath(createEmptyFile())
         ADD_DOMAINS(database, known_domains, cath_names, pfam_names)
         domains_h5 = ADD_DOMAINS.out.domains_h5
 
@@ -23,9 +28,6 @@ workflow DOMAINS {
 
 workflow {
     database = Channel.fromPath(params.database)
-    domains = Channel.fromPath("${params.known_domains}/*")
-    cath_names = Channel.fromPath(params.cath_names_path)
-    pfam_names = Channel.fromPath(params.pfam_names_path)
 
-    DOMAINS(database, domains, cath_names, pfam_names)
+    DOMAINS(database)
 }
diff --git a/workflows/oma_browser_build.nf b/workflows/oma_browser_build.nf
@@ -27,16 +27,9 @@ workflow OMA_BROWSER_BUILD {
                     vps_base,
                     EXTRACT_DARWIN.out.splice_json)
 
-        if (params.known_domains != null) {
-            domains = Channel.fromPath("${params.known_domains}/*")
-            cath_names = Channel.fromPath(params.cath_names_path)
-            pfam_names = Channel.fromPath(params.pfam_names_path)
+        // import Domains
+        DOMAINS(IMPORT_HDF5.out.db_h5)
 
-            DOMAINS(IMPORT_HDF5.out.db_h5, domains, cath_names, pfam_names)
-            domains_h5 = DOMAINS.out.domains_h5
-        } else {
-            domains_h5 = Channel.empty()
-        }
         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)
@@ -57,7 +50,7 @@ workflow OMA_BROWSER_BUILD {
                   gaf)
 
         h5_dbs_to_combine = IMPORT_HDF5.out.db_h5.mix(
-             domains_h5,
+             DOMAINS.out.domains_h5,
              GENERATE_XREFS.out.xref_db,
              GO_IMPORT.out.go_h5,
              CACHE_BUILDER.out.cache_h5,