improved join master

ktmeaton · Feb 28, 2020 · 926f817 · 926f817
1 parent 22e4e12
commit 926f817
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Showing 2 changed files with 17 additions and 2 deletions.
diff --git a/README.md b/README.md
@@ -104,6 +104,21 @@ params.ncbimeta_join_second_uniq = "'BioSampleBioProjectAccession'"
 params.ncbimeta_join_second_accessory = "'BioProject'"
 params.ncbimeta_join_second_anchor = "MasterFirst"
 
+NCBImetaJoin.py \
+  --database yersinia_pestis_db.sqlite \
+  --anchor BioSample \
+  --accessory "SRA" \
+  --final BioSampleSRA \
+  --unique "BioSampleAccession BioSampleSRAAccession"
+
+  NCBImetaJoin.py \
+    --database yersinia_pestis_db.sqlite \
+    --anchor Assembly \
+    --accessory "BioProject" \
+    --final AssemblyBioProject \
+    --unique "AssemblyAccession AssemblyGenbankBioprojectAccession"
+
+
 NCBImetaJoin.py \
   --database yersinia_pestis_db.sqlite \
   --anchor BioSample \
@@ -116,7 +131,7 @@ NCBImetaJoin.py \
   --anchor MasterFirst \
   --accessory BioProject \
   --final Master \
-  --unique ${params.ncbimeta_join_second_uniq}
+  --unique "BioSampleAccession BioSampleBioProjectAccession"
 
 ### Perl5 Issues
 export PERL5LIB=~/miniconda3/envs/phylo-env/lib/site_perl/5.26.2/
diff --git a/pipeline.nf b/pipeline.nf
@@ -107,7 +107,7 @@ params.ncbimeta_join_first_anchor = "BioSample"
 
 // NCBImetaJoin Second Parameters
 params.ncbimeta_join_second_final = "Master"
-params.ncbimeta_join_second_uniq = "'BioSampleBioProjectAccession'"
+params.ncbimeta_join_second_uniq = "'BioSampleAccession BioSampleBioProjectAccession'"
 params.ncbimeta_join_second_accessory = "'BioProject'"
 params.ncbimeta_join_second_anchor = "MasterFirst"