Fix #35 - markerset-based namespace for features

plantinformatics · Mar 21, 2020 · 3ede5d4 · 3ede5d4
1 parent 6c288e4
commit 3ede5d4
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git 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
@@ -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}" \