Project id then version and date for config generation logs, copy PED file...

Project id then version and date for config generation logs, copy PED file rather than symbolic links

docs/SOP_alignment_variant_annotation_ultra2.md

@@ -122,12 +122,12 @@ project_id=<project_id>
 source /home/u035/u035/shared/scripts/trio_whole_exome_config.sh
 ```
 
-2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, create a symlink with the correct name.
+2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, copy it instead.
 
 ```
 cd $PARAMS_DIR
 ped_file=<input_ped_file>
-ln -s $ped_file $project_id.ped
+cp $ped_file $project_id.ped
 ```
 
 3. In the params folder, create the symlinks to the reads and the bcbio configuration files. If specifying a common sample suffix, ensure it includes any joining characters, e.g. “-“ or “_”, so that the family identifier can be cleanly separated from the suffix. Get the number of families from the batch. Version should be "v1" by default for the first analysis run of a batch, "v2" etc for subsequent runs.
@@ -141,7 +141,7 @@ version=<version>
 sample_suffix=<sample_suffix>
 /home/u035/u035/shared/scripts/prepare_bcbio_config.sh \
   /home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
-  $project_id $version $sample_suffix &> ${version}_${project_id}.log
+  $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}'`
 ```
 
@@ -153,7 +153,7 @@ version=<version>
 sample_suffix=<sample_suffix>
 /home/u035/u035/shared/scripts/prepare_bcbio_config_crf.sh \
   /home/u035/u035/shared/scripts/trio_whole_exome_crf_config.sh \
-  $project_id $version $sample_suffix &> ${version}_${project_id}.log
+  $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}'`
 ```