Mapping to family ids improved

submit_trio_wes_bcbio.sh

 #!/bin/bash
-#SBATCH --cpus-per-task=32
+#SBATCH --cpus-per-task=16
 #SBATCH --mem=8GB
 #SBATCH --time=48:00:00
 #SBATCH --job-name=trio_whole_exome_bcbio
@@ -17,7 +17,8 @@ FAMILY_ID=`head -n $SLURM_ARRAY_TASK_ID $PARAMS_DIR/$PROJECT_ID.family_ids.txt |
 
 SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
 
-CONFIG_FILE=$CONFIG_DIR/${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}.yaml
+CONFIG_FILE=$CONFIG_DIR/*_${FAMILY_ID}.yaml
+
 mkdir -p $WORK_DIR/$FAMILY_ID
 cd $WORK_DIR/$FAMILY_ID
 

submit_trio_wes_cram_compression.sh

@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
 
 # This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be -
 # if there was a re-run of a family, it should have a new project id and version.
-cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
+cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*_${FAMILY_ID}
 
 for BAM in */*.bam
 do

submit_trio_wes_family_checksums.sh

@@ -19,7 +19,7 @@ SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
 
 # This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be -
 # if there was a re-run of a family, it should have a new project id and version.
-cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
+cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*_${FAMILY_ID}
 
 rm md5sum.txt 2> /dev/null