add replaces / replace_reason generation to trackhub manifest

diff --git a/htsworkflow/templates/manifest.txt b/htsworkflow/templates/manifest.txt
index adf055457f53d68f9ead81906614cd4415641c53..c81259cb77949fdffccb321f59e93634fc5e1540 100644 (file)
--- a/htsworkflow/templates/manifest.txt
+++ b/htsworkflow/templates/manifest.txt
@@ -1,2 +1,2 @@
-#file_name     format  output_type     experiment      replicate       enriched_in     ucsc_db{% for r in files %}
-{{ r.relative_path }}  {{ r.file_format }}     {{ r.output_type }}     {{ r.dataset_id }}      {{ r.replicate }}       {{ r.enriched_in }}     {{ r.ucsc_db }}{% endfor %}
+#file_name     format  output_type     experiment      replicate       enriched_in     ucsc_db replaces        replace_reason{% for r in files %}
+{{ r.relative_path }}  {{ r.file_format }}     {{ r.output_type }}     {{ r.dataset_id }}      {{ r.replicate }}       {{ r.enriched_in }}     {{ r.ucsc_db }} {{ r.replaces_accession|default_if_none:"" }}   {{ r.replace_reason|default_if_none:"" }}{% endfor %}

diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
index 1c83b4760b2b416553c91ebbc9b29f64bec38943..cb5c4fd5195b87302ddd6236f19ea2b16339f8cf 100644 (file)
--- a/htsworkflow/templates/trackhub_manifest.sparql
+++ b/htsworkflow/templates/trackhub_manifest.sparql
@@ -6,7 +6,7 @@ PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
 PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
 PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
 
-select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db
+select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db ?replaces_accession ?replace_reason
 WHERE {
   <{{submission}}> a submissionOntology:submission ;
                    submissionOntology:name ?name ;
@@ -17,6 +17,10 @@ WHERE {
         htswlib:library ?library ;
         a ?fileClass .
 
+  OPTIONAL { ?file encode3:replaces ?replaces_accession ;
+                   encode3:replace_reason ?replace_reason .
+  }
+
   ?fileClass geoSoft:fileTypeLabel ?file_format ;
              ucscDaf:output_type ?output_type .