push comment into config

broadinstitute · Apr 13, 2015 · cd7dce4 · cd7dce4
1 parent 2372f93
commit cd7dce4
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/pipes/config.json b/pipes/config.json
@@ -28,7 +28,8 @@
     "author_template":        "NCBI/authors.sbt",
     "source_modifier_table":  "NCBI/sample_meta.src",
     "biosample_map":          "NCBI/biosample-map.txt",
-    "sequencing_technology":  "Illumina HiSeq 2500; Nextera LC"
+    "sequencing_technology":  "Illumina HiSeq 2500; Nextera LC",
+    "comment":                "Please be aware that the annotation is done automatically with little or no manual curation."
   },
 
   "seq_center": "BI",

diff --git a/pipes/rules/interhost.rules b/pipes/rules/interhost.rules
@@ -99,7 +99,7 @@ rule prepare_genbank:
                 genbank_source_table=config.get('genbank',{}).get('source_modifier_table', ''),
                 biosample_map=config.get('genbank',{}).get('biosample_map', ''),
                 seq_tech=config.get('genbank',{}).get('sequencing_technology', 'unknown'),
-                comment='Please be aware that the annotation is done automatically with little or no manual curation.',
+                comment=config.get('genbank',{}).get('comment', ''),
                 logid="all"
     shell:
                 ' '.join(["{config[binDir]}/ncbi.py prep_genbank_files",