From 3ede5d4bb54412e56353319365c9907a6d94f0e5 Mon Sep 17 00:00:00 2001
From: Rad Suchecki <r.suchecki@gmail.com>
Date: Sat, 21 Mar 2020 11:55:08 +1100
Subject: [PATCH] Fix #35 - markerset-based namespace for features

---
 bin/paf2pretzel.groovy | 7 +++++--
 main.nf                | 1 +
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/bin/paf2pretzel.groovy b/bin/paf2pretzel.groovy
index b19e1d6..e683138 100755
--- a/bin/paf2pretzel.groovy
+++ b/bin/paf2pretzel.groovy
@@ -36,9 +36,12 @@ import static picocli.CommandLine.*
 @Option(names = ["--parent"], description = ["Parent dataset name"])
 @Field private String parent
 
-@Option(names = ["--base-name"], description = ["Basename used for dataset name/namespace"])
+@Option(names = ["--base-name"], description = ["Basename used for dataset name"])
 @Field private String basename
 
+@Option(names = ["--namespace"], description = ["String used for dataset namespace"])
+@Field private String namespace
+
 @Option(names = ["--short-name"], description = ["Short display name"])
 @Field private String shortName
 
@@ -83,7 +86,7 @@ annotation.meta = [:]
 
 annotation.'public' = !makePrivate
 annotation.name = "${basename}_${seqType}"
-annotation.namespace = basename
+annotation.namespace = namespace
 annotation.parent = parent
 annotation.meta.shortName = shortName
 if(alignTool != null && alignParams != null) {
diff --git a/main.nf b/main.nf
index 1fd54e7..bc2fced 100644
--- a/main.nf
+++ b/main.nf
@@ -181,6 +181,7 @@ process generateFeaturesFromSeqAlignmentsJSON {
     --parent ${genome} \
     --sequence-type ${meta.seqs.seqtype} \
     --base-name ${tag} \
+    --namespace ${meta.seqs.name} \
     --short-name ${meta.seqs.name} \
     --align-tool ${meta.align.tool} \
     --align-params "${meta.align.params}" \