diff --git a/workflows/run.nf b/workflows/run.nf
index bfdf433..3090d0c 100644
--- a/workflows/run.nf
+++ b/workflows/run.nf
@@ -85,9 +85,9 @@ workflow RUN {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"
diff --git a/workflows/run_validation.nf b/workflows/run_validation.nf
index 66e55ca..c0cdf32 100644
--- a/workflows/run_validation.nf
+++ b/workflows/run_validation.nf
@@ -43,9 +43,9 @@ workflow RUN_VALIDATION {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"