Aaaand another small change

wgbs-pipeline.sh

@@ -23,9 +23,9 @@ bowtie2="/usr/local/bin/bowtie2-2.4.41"
 bowtie_path="/opt/bowtie2-2.4.41/"
 samtools="/usr/local/bin/samtools-1.10"
 samtools_path="/opt/samtools-1.10"
-ext_chr_srt=$( realpath ${PIPELINEPATH}/apps/ext_chr_srt.py )
-meth_prop=$( realpath ${PIPELINEPATH}/apps/methylation_proportion.py )
-generate_bs_indices="./apps/generate_bs_indices.sh"
+ext_chr_srt="${PIPELINEPATH}/apps/ext_chr_srt.py"
+meth_prop="${PIPELINEPATH}/apps/methylation_proportion.py"
+generate_bs_indices="${PIPELINEPATH}/apps/generate_bs_indices.sh"
 
 psrecord="~/.local/bin/psrecord"