Fixed paths, needed abs path for MultiQC

docs/SOP_alignment_variant_annotation.md

@@ -198,7 +198,7 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 4. Submit the bcbio jobs from the logs folder.
 
 ```
-cd /home/u035/project/trio_whole_exome/logs
+cd /home/u035/project/trio_whole_exome/analysis/logs
 qsub -v PROJECT_ID=$project_id,\
   CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
   -J 1-$X -N trio_whole_exome_bcbio.$project_id \
@@ -211,8 +211,8 @@ If all log files end in ‘Finished’ or ‘Storing in local filesystem’ for
 
 ```
 source /home/u035/project/scripts/trio_whole_exome_config.sh
-cd /scratch/u035/project/trio_whole_exome/output
-multiqc --title "Trio whole exome QC report: $project_id" \
+cd /scratch/u035/project/trio_whole_exome/analysis/output
+/home/u035/project/software/bcbio/anaconda/bin/multiqc --title "Trio whole exome QC report: $project_id" \
   --outdir qc \
   --filename ${project_id}_qc_report.html \
   *$project_id*