diff --git a/analyses/methylation-summary/tools/01-create-probe-annotations.cwl b/analyses/methylation-summary/tools/01-create-probe-annotations.cwl
index 30c09bdcd0..b9c5d0bb53 100644
--- a/analyses/methylation-summary/tools/01-create-probe-annotations.cwl
+++ b/analyses/methylation-summary/tools/01-create-probe-annotations.cwl
@@ -29,10 +29,14 @@ arguments:
       ./.git
       mkdir -p analyses/methylation-summary/results/
       Rscript 01-create-probe-annotations.R
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }
 
diff --git a/analyses/methylation-summary/tools/02-calculate-methly-quantiles.cwl b/analyses/methylation-summary/tools/02-calculate-methly-quantiles.cwl
index 6c7da8e071..41a6ee5f19 100644
--- a/analyses/methylation-summary/tools/02-calculate-methly-quantiles.cwl
+++ b/analyses/methylation-summary/tools/02-calculate-methly-quantiles.cwl
@@ -29,10 +29,14 @@ arguments:
       ./.git
       mkdir -p analyses/methylation-summary/results/
       Rscript 02-calculate-methly-quantiles.R
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }
 
diff --git a/analyses/methylation-summary/tools/03-methyl-tpm-correlation.cwl b/analyses/methylation-summary/tools/03-methyl-tpm-correlation.cwl
index 4eedf0263a..0f50ada860 100644
--- a/analyses/methylation-summary/tools/03-methyl-tpm-correlation.cwl
+++ b/analyses/methylation-summary/tools/03-methyl-tpm-correlation.cwl
@@ -32,10 +32,14 @@ arguments:
       touch ./.git/HEAD
       mkdir -p analyses/methylation-summary/results
       python3 03-methyl-tpm-correlation.py
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }
 
diff --git a/analyses/methylation-summary/tools/04-tpm-transcript-representation.cwl b/analyses/methylation-summary/tools/04-tpm-transcript-representation.cwl
index 82e180644c..ca4d959855 100644
--- a/analyses/methylation-summary/tools/04-tpm-transcript-representation.cwl
+++ b/analyses/methylation-summary/tools/04-tpm-transcript-representation.cwl
@@ -32,10 +32,14 @@ arguments:
       touch ./.git/HEAD
       mkdir -p analyses/methylation-summary/results
       python3 04-tpm-transcript-representation.py
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }
 
diff --git a/analyses/methylation-summary/tools/05-create-methyl-summary-table.cwl b/analyses/methylation-summary/tools/05-create-methyl-summary-table.cwl
index da7ce5c9db..430ceb0923 100644
--- a/analyses/methylation-summary/tools/05-create-methyl-summary-table.cwl
+++ b/analyses/methylation-summary/tools/05-create-methyl-summary-table.cwl
@@ -29,10 +29,14 @@ arguments:
       ./.git
       mkdir -p analyses/methylation-summary/results/
       Rscript 05-create-methyl-summary-table.R
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }
 
diff --git a/analyses/methylation-summary/tools/06-methly-summary-tsv2jsonl.cwl b/analyses/methylation-summary/tools/06-methly-summary-tsv2jsonl.cwl
index 49eff4ae78..e28680bd91 100644
--- a/analyses/methylation-summary/tools/06-methly-summary-tsv2jsonl.cwl
+++ b/analyses/methylation-summary/tools/06-methly-summary-tsv2jsonl.cwl
@@ -32,10 +32,14 @@ arguments:
       touch ./.git/HEAD
       mkdir -p analyses/methylation-summary/results
       python3 06-methly-summary-tsv2jsonl.py
+  - position: 99
+    shellQuote: false
+    valueFrom: |-
       ${
           if (inputs.output_basename != null) {
-             var cmd = "for f in analyses/methylation-summary/results/*; do mv \"$f\" \"" + output_basename + "-$f \"; done";
-             return cmd;
+            var cmd = " && cd analyses/methylation-summary/results/ && ";
+            cmd += "for f in *; do mv \"$f\" \"" + inputs.output_basename + "-$f \"; done";
+            return cmd;
           }
       }