From 797e0a1f7785cf8b943d0e4df6a8d8c460813ca2 Mon Sep 17 00:00:00 2001
From: Adrian Altenhoff <adrian.altenhoff@inf.ethz.ch>
Date: Thu, 16 Jan 2025 13:32:58 +0100
Subject: [PATCH] [FIX] working with 0-* domains files

---
 modules/local/domains/main.nf      | 7 +++----
 subworkflows/local/domains/main.nf | 7 +++----
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/modules/local/domains/main.nf b/modules/local/domains/main.nf
index f960f09..6af399a 100644
--- a/modules/local/domains/main.nf
+++ b/modules/local/domains/main.nf
@@ -14,13 +14,12 @@ process ADD_DOMAINS {
         path "domains.h5", emit: domains_h5
 
     script:
-        def domains = ($domain_files.name != "NO_FILE") ? "--domains $domain_files" : ''
         """
         oma-build -vv domains \\
             --db $database \\
             --hdf5-out domains.h5 \\
-            $domains \\
-            --cath-names $cath_names \
+            --domains $domain_files \\
+            --cath-names $cath_names \\
             --pfam-names $pfam_names
         """
 
@@ -28,4 +27,4 @@ process ADD_DOMAINS {
         """
         touch domains.h5
         """
-}
\ No newline at end of file
+}
diff --git a/subworkflows/local/domains/main.nf b/subworkflows/local/domains/main.nf
index a66f447..bbde205 100644
--- a/subworkflows/local/domains/main.nf
+++ b/subworkflows/local/domains/main.nf
@@ -10,18 +10,17 @@ workflow DOMAINS {
     main:
         // TODO should be extended to include computation of new domain annotation
         // for unknown sequences
-        known_domains = (params.known_domains != null) ? Channel.fromPath("${params.known_domains}/*").collect() : Channel.fromPath("$projectDir/assets/NO_FILE")
+        known_domains = (params.known_domains != null) ? Channel.fromPath("${params.known_domains}/*").collect() : []
         cath_names = (params.cath_names_path != null) ? Channel.fromPath(params.cath_names_path) : Channel.fromPath("$projectDir/assets/NO_FILE")
         pfam_names = (params.pfam_names_path != null) ? Channel.fromPath(params.pfam_names_path) : Channel.fromPath("$projectDir/assets/NO_FILE")
         ADD_DOMAINS(database, known_domains, cath_names, pfam_names)
-        domains_h5 = ADD_DOMAINS.out.domains_h5
 
     emit:
-        domains_h5
+        domains_h5 = ADD_DOMAINS.out.domains_h5
 }
 
 workflow {
     database = Channel.fromPath(params.database)
 
     DOMAINS(database)
-}
\ No newline at end of file
+}