project.* to pipeline.* config updates (#80)

Author: mikesioda

resources/config/default/docker.properties

@@ -12,7 +12,7 @@ kneaddata.dbs=/db
 kraken.db=/db
 kraken2.db=/db
 
-project.defaultProps=$BLJ/resources/config/default/standard.properties
+pipeline.defaultProps=$BLJ/resources/config/default/standard.properties
 
 #rdp.db=/db/rRNAClassifier.properties
 rdp.jar=/app/classifier.jar

resources/config/template/kraken2Template.properties

@@ -21,7 +21,7 @@ input.trimSuffix=.fq
 
 metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
 
-project.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 
 r.nominalFields=ruralUrban
 r.timeout=20

resources/config/template/krakenTemplate.properties

@@ -21,7 +21,7 @@ input.trimSuffix=.fq
 
 metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
 
-project.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 
 r.nominalFields=ruralUrban
 r.timeout=20

resources/config/template/metaphlan2Template.properties

@@ -17,7 +17,7 @@ input.trimSuffix=.fq
 
 metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
 
-project.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 
 r.nominalFields=ruralUrban
 r.timeout=20

resources/config/template/qiimeTemplate.properties

@@ -23,7 +23,7 @@ input.trimSuffix=.fq
 
 metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
 
-project.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 
 r.nominalFields=ruralUrban
 

resources/config/template/rdpTemplate.properties

@@ -21,7 +21,7 @@ input.trimSuffix=.fq
 
 metadata.filePath=$BLJ_SUP/resources/metadata/chinaMetadata.tsv
 
-project.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
+pipeline.defaultProps=$BLJ_SUP/resources/config/default/copperhead.properties
 
 r.nominalFields=ruralUrban
 

resources/log4j.properties

@@ -1,7 +1,7 @@
  # log4j.properties 
 
 # Set log level and targets
-log4j.rootLogger=${project.logLevel}, file, stdout
+log4j.rootLogger=${pipeline.logLevel}, file, stdout
 
 # Command line output
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender