Corrected and simplified file paths for ultra2

trio_whole_exome_config.sh

@@ -3,19 +3,22 @@
 # Basic configuration options for trio WES pipeline
 #
 
-SCRIPTS=/home/u035/u035/shared/scripts
-BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
-TARGET=/home/u035/u035/shared/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-DOWNLOAD_DIR=/scratch/u035/u035/shared/data
-REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
+# primary locations
+BASE=/home/u035/u035/shared
+SCRIPTS=$BASE/scripts
+DOWNLOAD_DIR=$BASE/data
+OUTPUT_DIR=$BASE/results
 
-BASE=/scratch/u035/u035/shared/analysis
-PARAMS_DIR=$BASE/params
-READS_DIR=$BASE/reads
-CONFIG_DIR=$BASE/config
-WORK_DIR=$BASE/work
-OUTPUT_DIR=$BASE/output
+# resource locations
+BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
+TARGET=$BASE/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+REFERENCE_GENOME=$BASE/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
-ARCHIVE_DIR=/archive/u035/trio_whole_exome
+# temporary working files
+PARAMS_DIR=$BASE/analysis/params
+READS_DIR=$BASE/analysis/reads
+CONFIG_DIR=$BASE/analysis/config
+WORK_DIR=$BASE/analysis/work
+LOGS_DIR=$BASE/analysis/logs
 
-export PATH=/home/u035/u035/shared/software/bcbio/tools/bin:$PATH
+export PATH=$BASE/software/bcbio/tools/bin:$PATH