Renaming prepare bcbio config scripts for consistency

docs/SOP_alignment_variant_annotation.md

@@ -140,7 +140,7 @@ cp $ped_file $project_id.ped
 ```
 cd $PARAMS_DIR
 sample_suffix=<sample_suffix>
-$SCRIPTS/prepare_bcbio_config.sh \
+$SCRIPTS/trio_wes_prepare_bcbio_config.sh \
   $SCRIPTS/trio_whole_exome_config.sh \
   $project_id $version $sample_suffix &> ${project_id}_${version}_`date +%Y%m%d%H%M`.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
@@ -151,7 +151,7 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
 cd $PARAMS_DIR
 sample_suffix=<sample_suffix>
-$SCRIPTS/scripts/prepare_bcbio_config_crf.sh \
+$SCRIPTS/scripts/trio_wes_prepare_bcbio_config_crf.sh \
   $SCRIPTS/trio_whole_exome_crf_config.sh \
   $project_id $version $sample_suffix &> ${project_id}_${version}_`date +%Y%m%d%H%M`.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
@@ -162,8 +162,7 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
 cd $LOGS_DIR
 sbatch --export=PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=$SCRIPTS/trio_whole_exome_config.sh \
-  --array=1-$X --job-name=trio_whole_exome_bcbio.$short_project_id \
-  $SCRIPTS/submit_bcbio_trio_wes.sh
+  --array=1-$X $SCRIPTS/submit_trio_wes_bcbio.sh
 ```
 
 If all log files end in ‘Finished’ or ‘Storing in local filesystem’ for a metadata file (occasionally the job completes without quite outputting all of the ‘Storing’ messages), the batch is complete. If this is not the case, resubmit the incomplete jobs – they will resume where they left off.