diff --git a/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh b/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh
index 86bbc15..f3f7e1a 100644
--- a/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh
+++ b/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh
@@ -26,7 +26,7 @@ do
     for patient in ${patients[@]} 
     do
         Rscript /hot/users/psteinberg/work-code/parse_consensus_tree_PhyloWGS.R \
-        -s /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.1.0/${patient}/PhyloWGS-2205be1/output/PhyloWGS-2205be1_${seed}_${patient}_SomaticSniper-Battenberg.summ.json.gz \
+        -s /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.1.0/"${patient}"/PhyloWGS-2205be1/output/PhyloWGS-2205be1_"${seed}"_"${patient}"_SomaticSniper-Battenberg.summ.json.gz \
         -o /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/consensus_tree
     done
 done
diff --git a/src/output-analysis/plotting/plotting_workflow.sh b/src/output-analysis/plotting/plotting_workflow.sh
index 6a5b9b6..f12e819 100644
--- a/src/output-analysis/plotting/plotting_workflow.sh
+++ b/src/output-analysis/plotting/plotting_workflow.sh
@@ -2,16 +2,16 @@
 projectdir=/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/
 workdir=/hot/user/yiyangliu/repo/project-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed/src/output-analysis/plotting/
 
-cd ${workdir}
+cd ${workdir} || exit
 for snv in Strelka2 Mutect2 SomaticSniper; do echo ${snv}
     for src in DPClust PhyloWGS PyClone-VI; do echo ${src}
         for mode in sr mr; do echo ${mode}
-            snvl=${snv,,}; echo ${snvl}
-            srcl=${src,,}; echo ${srcl}
-            file=$(ls ${projectdir}/pipeline-call-src/run-${snvl}-battenberg-${srcl}/output/*${snvl}_battenberg_${srcl}_${mode}.tsv -Art | tail -n 1)
-            echo ${file}
+            snvl=${snv,,}; echo "${snvl}"
+            srcl=${src,,}; echo "${srcl}"
+            file=$(ls ${projectdir}/pipeline-call-src/run-"${snvl}"-battenberg-"${srcl}"/output/*"${snvl}"_battenberg_"${srcl}"_${mode}.tsv -Art | tail -n 1)
+            echo "${file}"
             if [ -f "$file" ]; then
-                Rscript ${workdir}/subclone_relative_seed_variability.R -f ${file} -p ${snv}-Battenberg-${src} -m ${mode} -o ${projectdir}/pipeline-call-src/plots/stripplot2
+                Rscript ${workdir}/subclone_relative_seed_variability.R -f "${file}" -p ${snv}-Battenberg-${src} -m ${mode} -o ${projectdir}/pipeline-call-src/plots/stripplot2
             fi
         done
     done
diff --git a/src/run-pipeline-call-src/mr_mutect2_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/mr_mutect2_battenberg_pyclone-vi_submission_script.sh
index 1f3bc95..65853cb 100644
--- a/src/run-pipeline-call-src/mr_mutect2_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/mr_mutect2_battenberg_pyclone-vi_submission_script.sh
@@ -20,7 +20,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 30
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -29,9 +29,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/multi-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Mutect2-Battenberg-PyClone-VI-mr \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/multi-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Mutect2-Battenberg-PyClone-VI-mr \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/mr_somaticsniper_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/mr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
index 323ca87..7a25116 100644
--- a/src/run-pipeline-call-src/mr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/mr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
@@ -20,7 +20,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 30
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -29,9 +29,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/multi-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_SomaticSniper-Battenberg-PyClone-VI-mr \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/multi-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_SomaticSniper-Battenberg-PyClone-VI-mr \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/mr_strelka2_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/mr_strelka2_battenberg_pyclone-vi_submission_script.sh
index 4ab40a2..4a08204 100644
--- a/src/run-pipeline-call-src/mr_strelka2_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/mr_strelka2_battenberg_pyclone-vi_submission_script.sh
@@ -20,7 +20,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 60
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -29,9 +29,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/multi-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Strelka2-Battenberg-PyClone-VI-mr \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/multi-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Strelka2-Battenberg-PyClone-VI-mr \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_mutect2_battenberg_dpclust_submission_script.sh b/src/run-pipeline-call-src/sr_mutect2_battenberg_dpclust_submission_script.sh
index 9777a28..770a9a4 100644
--- a/src/run-pipeline-call-src/sr_mutect2_battenberg_dpclust_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_mutect2_battenberg_dpclust_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 240
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-dpclust/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Mutect2-Battenberg-DPClust-sr \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-dpclust/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Mutect2-Battenberg-DPClust-sr \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_mutect2_battenberg_phylowgs_submission_script.sh b/src/run-pipeline-call-src/sr_mutect2_battenberg_phylowgs_submission_script.sh
index 1817ebf..a904b1e 100644
--- a/src/run-pipeline-call-src/sr_mutect2_battenberg_phylowgs_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_mutect2_battenberg_phylowgs_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 30
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 6 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/software/pipeline/pipeline-call-SRC/Nextflow/release/1.0.0-rc.1/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Mutect2-Battenberg-PhyloWGS \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Mutect2-Battenberg-PhyloWGS \
             --partition_type F72 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_mutect2_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/sr_mutect2_battenberg_pyclone-vi_submission_script.sh
index 50a8952..7755446 100644
--- a/src/run-pipeline-call-src/sr_mutect2_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_mutect2_battenberg_pyclone-vi_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 30
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Mutect2-Battenberg-PyClone-VI \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Mutect2-Battenberg-PyClone-VI \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_dpclust_submission_script.sh b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_dpclust_submission_script.sh
index 887914e..7f71e6c 100644
--- a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_dpclust_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_dpclust_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 240
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-dpclust/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_SomaticSniper-Battenberg-DPClust \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-dpclust/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_SomaticSniper-Battenberg-DPClust \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_phylowgs_submission_script.sh b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_phylowgs_submission_script.sh
index 173619b..0da5c14 100644
--- a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_phylowgs_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_phylowgs_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 60
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_SomaticSniper-Battenberg-PhyloWGS-sr \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_SomaticSniper-Battenberg-PhyloWGS-sr \
             --partition_type F72 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
index f1c990e..5ef285a 100644
--- a/src/run-pipeline-call-src/sr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_somaticsniper_battenberg_pyclone-vi_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 60
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_SomaticSniper-Battenberg-PyClone-VI \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_SomaticSniper-Battenberg-PyClone-VI \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_strelka2_battenberg_dpclust_submission_script.sh b/src/run-pipeline-call-src/sr_strelka2_battenberg_dpclust_submission_script.sh
index 912b956..5dc8bb4 100644
--- a/src/run-pipeline-call-src/sr_strelka2_battenberg_dpclust_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_strelka2_battenberg_dpclust_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 240
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-dpclust/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Strelka2-Battenberg-DPClust \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-dpclust/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Strelka2-Battenberg-DPClust \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_strelka2_battenberg_phylowgs_submission_script.sh b/src/run-pipeline-call-src/sr_strelka2_battenberg_phylowgs_submission_script.sh
index 727ccf1..acdfabc 100644
--- a/src/run-pipeline-call-src/sr_strelka2_battenberg_phylowgs_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_strelka2_battenberg_phylowgs_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 300
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 6 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/software/pipeline/pipeline-call-SRC/Nextflow/release/1.0.0-rc.1/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Strelka2-Battenberg-PhyloWGS \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Strelka2-Battenberg-PhyloWGS \
             --partition_type F72 \
             --email psteinberg@mednet.ucla.edu
     done
diff --git a/src/run-pipeline-call-src/sr_strelka2_battenberg_pyclone-vi_submission_script.sh b/src/run-pipeline-call-src/sr_strelka2_battenberg_pyclone-vi_submission_script.sh
index 6eede0d..15ce8e2 100644
--- a/src/run-pipeline-call-src/sr_strelka2_battenberg_pyclone-vi_submission_script.sh
+++ b/src/run-pipeline-call-src/sr_strelka2_battenberg_pyclone-vi_submission_script.sh
@@ -27,7 +27,7 @@ do
         while [ $submit_signal == "false" ]
         do
             sleep 60
-            jobs_running=$((`squeue -u psteinberg | wc -l` - 1))
+            jobs_running=$(($(squeue -u psteinberg | wc -l) - 1))
             echo "jobs running: $jobs_running"
             if [ $jobs_running -lt 5 ]
             then
@@ -36,9 +36,9 @@ do
         done
         python3 /hot/software/package/tool-submit-nf/Python/release/2.2.0/submit_nextflow_pipeline.py \
             --nextflow_script /hot/user/yashpatel/pipeline-call-SRC/pipeline-call-SRC/main.nf \
-            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/input/config/seed_${seed}.config \
-            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/${patient}.yaml \
-            --pipeline_run_name ${patient}_${seed}_Strelka2-Battenberg-PyClone-VI \
+            --nextflow_config /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/input/config/seed_"${seed}".config \
+            --nextflow_yaml /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/"${patient}".yaml \
+            --pipeline_run_name "${patient}"_"${seed}"_Strelka2-Battenberg-PyClone-VI \
             --partition_type F32 \
             --email psteinberg@mednet.ucla.edu
     done