diff --git a/CHANGELOG.md b/CHANGELOG.md
index bac73786..9d31f500 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,25 @@
+# htrnaseq v0.12.2
+
+## Bug fixes
+
+* Avoid duplicate input paths when publishing results (PR #76).
+
+# htrnaseq v0.12.1
+
+# Minor changes
+
+* Update `parallel_map` cpu label from `lowcpu` to `highcpu` (PR 75).
+
+# htrnaseq v0.12.0
+
+# Minor changes
+
+* Improve publishing speed by keeping symbolic links (PR #74).
+
+# Bug fixes
+
+* Avoid double slashes in the publish directory path in order to not create empty objects on S3 (PR #72).
+
 # htrnaseq v0.11.0
 
 ## Breaking changes
diff --git a/src/io/publish_fastqs/code.sh b/src/io/publish_fastqs/code.sh
index 4ee3c658..f7ad32be 100755
--- a/src/io/publish_fastqs/code.sh
+++ b/src/io/publish_fastqs/code.sh
@@ -11,5 +11,5 @@ echo "Copying files..."
 IFS=";" read -ra input <<<$par_input
 
 for i in "${input[@]}"; do
-  cp -rL "$i" "$par_output/"
+  cp -a --keep-directory-symlink "$i" "$par_output/"
 done
\ No newline at end of file
diff --git a/src/io/publish_results/code.sh b/src/io/publish_results/code.sh
index 62349343..e3a4242e 100755
--- a/src/io/publish_results/code.sh
+++ b/src/io/publish_results/code.sh
@@ -7,87 +7,60 @@ echo "Publishing results to multiple output directories"
 # Create output directories for multiple files
 echo "Creating output directories..."
 
-path_pars=(
-  par_star_output_dir
-  par_nrReadsNrGenesPerChrom_dir
-  par_star_qc_metrics_dir
-  par_eset_dir
-  par_f_data_dir
-  par_p_data_dir
-  par_html_report_output
-  par_run_params_output
+declare -A path_pars_dirs=(
+  ["par_star_output_dir"]="par_star_output"
+  ["par_nrReadsNrGenesPerChrom_dir"]="par_nrReadsNrGenesPerChrom"
+  ["par_star_qc_metrics_dir"]="par_star_qc_metrics"
+  ["par_eset_dir"]="par_eset"
+  ["par_f_data_dir"]="par_f_data"
+  ["par_p_data_dir"]="par_p_data"
 )
 
-for par in ${path_pars[@]}; do
+declare -A path_pars_files=(
+  ["par_html_report_output"]="par_html_report"
+  ["par_run_params_output"]="par_run_params"
+)
+
+echo "Canonicalizing output paths."
+all_path_args=( "${!path_pars_files[@]}" "${!path_pars_dirs[@]}" )
+for par in ${all_path_args[@]}; do
     curr_val="${!par}"
+    printf "\t%s\n" "Canonicalizing path '$curr_val'"
     new_value=$(realpath --canonicalize-missing "$curr_val")
+    printf "\t%s\n" "New output path for '$par': '$new_value'"
     declare -g "$par=$new_value"
 done
 
-mkdir -p "$par_star_output_dir" && echo "$par_star_output_dir created"
-mkdir -p "$par_nrReadsNrGenesPerChrom_dir" && echo "$par_nrReadsNrGenesPerChrom_dir created"  
-mkdir -p "$par_star_qc_metrics_dir" && echo "$par_star_qc_metrics_dir created"
-mkdir -p "$par_eset_dir" && echo "$par_eset_dir created"
-mkdir -p "$par_f_data_dir" && echo "$par_f_data_dir created"
-mkdir -p "$par_p_data_dir" && echo "$par_p_data_dir created"
-
-echo
-echo "Copying STAR output files..."
-IFS=";" read -ra star_output <<<$par_star_output
-for i in "${star_output[@]}"; do
-  echo "Copying $i to $par_star_output_dir/"
-  cp -rL "$i" "$par_star_output_dir/"
+echo "Creating output directories"
+for par in ${!path_pars_dirs[@]}; do
+    curr_val="${!par}"
+    mkdir -p "$curr_val" && printf "\t%s\n" "$curr_val created."
+done
+for par in ${!path_pars_files[@]}; do
+    curr_val="${!par}"
+    file_dir=$(dirname "$curr_val")
+    mkdir -p "$file_dir" && printf "\t%s\n" "$file_dir created."
 done
 
-echo
-echo "Copying nrReadsNrGenesPerChrom files..."
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<$par_nrReadsNrGenesPerChrom
-for i in "${nrReadsNrGenesPerChrom[@]}"; do
-  echo "Copying $i to $par_nrReadsNrGenesPerChrom_dir/"
-  cp -rL "$i" "$par_nrReadsNrGenesPerChrom_dir/"
+echo "Copying output for inputs that are directories"
+for par in ${!path_pars_dirs[@]}; do
+  printf "\t%s\n" "Copying output for '$par'"
+  output_val="${!par}"
+  input_par_name="${path_pars_dirs[${par}]}"
+  input_val="${!input_par_name}"
+  IFS=";" read -ra output_files_list <<<$input_val
+  for i in "${output_files_list[@]}"; do 
+      printf "\t%s\n" "Copying '$i' to '$output_val'" 
+      cp -a --keep-directory-symlink "$i" "$output_val/"
+  done
 done
 
-echo
-echo "Copying STAR QC metrics files..."
-IFS=";" read -ra star_qc_metrics <<<$par_star_qc_metrics
-for i in "${star_qc_metrics[@]}"; do
-  echo "Copying $i to $par_star_qc_metrics_dir/"
-  cp -rL "$i" "$par_star_qc_metrics_dir/"
-done
-
-echo
-echo "Copying eset files..."
-IFS=";" read -ra eset <<<$par_eset
-for i in "${eset[@]}"; do
-  echo "Copying $i to $par_eset_dir/"
-  cp -rL "$i" "$par_eset_dir/"
-done
-
-echo
-echo "Copying f_data files..."
-IFS=";" read -ra f_data <<<$par_f_data
-for i in "${f_data[@]}"; do
-  echo "Copying $i to $par_f_data_dir/"
-  cp -rL "$i" "$par_f_data_dir/"
-done
-
-echo
-echo "Copying p_data files..."
-IFS=";" read -ra p_data <<<$par_p_data
-for i in "${p_data[@]}"; do
-  echo "Copying $i to $par_p_data_dir/"
-  cp -rL "$i" "$par_p_data_dir/"
-done
-
-echo
 echo "Copying single files directly..."
-mkdir -p $(dirname "$par_html_report_output")
-echo "Copying $par_html_report to $par_html_report_output"
-cp -L "$par_html_report" "$par_html_report_output"
+for par in ${!path_pars_files[@]}; do
+  output_val="${!par}"
+  input_par_name="${path_pars_files[${par}]}"
+  input_val="${!input_par_name}"
+  cp -a --keep-directory-symlink "$input_val" "$output_val"
+done
 
-echo "Copying $par_run_params to $par_run_params_output"
-mkdir -p $(dirname "$par_run_params_output")
-cp -L "$par_run_params" "$par_run_params_output"
-
-echo
 echo "Publishing completed successfully!"
diff --git a/src/workflows/htrnaseq/main.nf b/src/workflows/htrnaseq/main.nf
index 6b7fb1a4..b164026f 100644
--- a/src/workflows/htrnaseq/main.nf
+++ b/src/workflows/htrnaseq/main.nf
@@ -146,7 +146,7 @@ workflow run_wf {
         return [id, new_state]
       } 
       | parallel_map.run(
-        directives: ["label": ["highmem", "lowcpu"]],
+        directives: ["label": ["highmem", "highcpu"]],
         fromState: {id, state ->
           [
             "input_r1": state.input_r1,
diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf
index 9e725d0d..f886665e 100644
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -3,6 +3,16 @@ def date = new Date().format('yyyyMMdd_hhmmss')
 def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
+if (!params.containsKey("results_publish_dir") || !params.containsKey("fastq_publish_dir")) {
+   error "Please set both 'results_publish_dir' and 'fastq_publish_dir'."
+}
+
+// S3 paths containing double slashes might cause issues with empty objects being created
+// Remove trailing slashes from the publish dir. The params map is immutable, so create a copy
+def regex_trailing_slashes = ~/\/+$/
+def results_publish_dir = params.results_publish_dir - regex_trailing_slashes
+def fastq_publish_dir = params.fastq_publish_dir - regex_trailing_slashes
+
 workflow run_wf {
   take:
     raw_ch
@@ -156,7 +166,7 @@ workflow run_wf {
               assert star_sample_dir.name == state.sample_id: "Unexpected state: the parent directory of STAR output \
                 path '${it}' should match with the sample ID ${sample_id}"
               star_sample_dir
-            }
+            }.unique()
           }
           def new_state = [
             "star_output": star_output_samples,
@@ -205,7 +215,7 @@ workflow run_wf {
         fromState: { id, state ->
           def prefix = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
 
-          println("Publising results to ${params.results_publish_dir}/${prefix}")
+          println("Publising results to ${results_publish_dir}/${prefix}")
 
           [ 
             // Inputs
@@ -231,7 +241,7 @@ workflow run_wf {
         toState: { id, result, state -> result + ["run_params": state.run_params] },
         directives: [
           publishDir: [
-            path: "${params.results_publish_dir}", 
+            path: results_publish_dir, 
             overwrite: false,
             mode: "copy"
           ]
@@ -278,7 +288,7 @@ workflow run_wf {
         toState: { id, result, state -> state },
         directives: [
           publishDir: [
-            path: "${params.fastq_publish_dir}", 
+            path: fastq_publish_dir, 
             overwrite: false,
             mode: "copy"
           ]
diff --git a/src/workflows/runner/test.nf b/src/workflows/runner/test.nf
index 85b2b9d3..a389ddde 100644
--- a/src/workflows/runner/test.nf
+++ b/src/workflows/runner/test.nf
@@ -107,7 +107,7 @@ workflow test_wf {
         assert output_state.eset_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.rds", "VH02001614.rds"].toSet()
         assert output_state.star_output_dir.listFiles().collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
         ["VH02001612", "VH02001614"].each{it ->
-           assert output_state.star_output_dir.resolve(it).listFiles().collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+           assert output_state.star_output_dir.resolve(it).toRealPath().listFiles().collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
         }
         assert output_state.star_qc_metrics_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
         assert output_state.nrReadsNrGenesPerChrom_dir.listFiles().collect{it.name}.toSet() == ["VH02001612.txt", "VH02001614.txt"].toSet()
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index 8bb1206a..f9acf6f0 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index fa6de78a..e920f43f 100755
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index f0929933..965f58e1 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index 18e988f6..c158fa3c 100755
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index c045b8ba..d4b141bf 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index a9486fb5..048e40e3 100755
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 2f63e01b..0c572ed6 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,7 +155,7 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
index c438e2f4..e78e4675 100755
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index 1223226f..fabd89c2 100644
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -164,7 +164,7 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
index 739a9da7..9bbe009f 100755
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml
index 20898f28..566395ef 100644
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -139,7 +139,7 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs
index 9b54392a..19a07fb2 100755
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -1093,7 +1093,7 @@ echo "Copying files..."
 IFS=";" read -ra input <<<\$par_input
 
 for i in "\${input[@]}"; do
-  cp -rL "\$i" "\$par_output/"
+  cp -a --keep-directory-symlink "\$i" "\$par_output/"
 done
 VIASHMAIN
 bash "\$tempscript" &
diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml
index 17cc4d19..4d204c4f 100644
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results
index 35613602..0da6c7ec 100755
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -1569,89 +1569,62 @@ echo "Publishing results to multiple output directories"
 # Create output directories for multiple files
 echo "Creating output directories..."
 
-path_pars=(
-  par_star_output_dir
-  par_nrReadsNrGenesPerChrom_dir
-  par_star_qc_metrics_dir
-  par_eset_dir
-  par_f_data_dir
-  par_p_data_dir
-  par_html_report_output
-  par_run_params_output
+declare -A path_pars_dirs=(
+  ["par_star_output_dir"]="par_star_output"
+  ["par_nrReadsNrGenesPerChrom_dir"]="par_nrReadsNrGenesPerChrom"
+  ["par_star_qc_metrics_dir"]="par_star_qc_metrics"
+  ["par_eset_dir"]="par_eset"
+  ["par_f_data_dir"]="par_f_data"
+  ["par_p_data_dir"]="par_p_data"
 )
 
-for par in \${path_pars[@]}; do
+declare -A path_pars_files=(
+  ["par_html_report_output"]="par_html_report"
+  ["par_run_params_output"]="par_run_params"
+)
+
+echo "Canonicalizing output paths."
+all_path_args=( "\${!path_pars_files[@]}" "\${!path_pars_dirs[@]}" )
+for par in \${all_path_args[@]}; do
     curr_val="\${!par}"
+    printf "\\t%s\\n" "Canonicalizing path '\$curr_val'"
     new_value=\$(realpath --canonicalize-missing "\$curr_val")
+    printf "\\t%s\\n" "New output path for '\$par': '\$new_value'"
     declare -g "\$par=\$new_value"
 done
 
-mkdir -p "\$par_star_output_dir" && echo "\$par_star_output_dir created"
-mkdir -p "\$par_nrReadsNrGenesPerChrom_dir" && echo "\$par_nrReadsNrGenesPerChrom_dir created"  
-mkdir -p "\$par_star_qc_metrics_dir" && echo "\$par_star_qc_metrics_dir created"
-mkdir -p "\$par_eset_dir" && echo "\$par_eset_dir created"
-mkdir -p "\$par_f_data_dir" && echo "\$par_f_data_dir created"
-mkdir -p "\$par_p_data_dir" && echo "\$par_p_data_dir created"
-
-echo
-echo "Copying STAR output files..."
-IFS=";" read -ra star_output <<<\$par_star_output
-for i in "\${star_output[@]}"; do
-  echo "Copying \$i to \$par_star_output_dir/"
-  cp -rL "\$i" "\$par_star_output_dir/"
+echo "Creating output directories"
+for par in \${!path_pars_dirs[@]}; do
+    curr_val="\${!par}"
+    mkdir -p "\$curr_val" && printf "\\t%s\\n" "\$curr_val created."
+done
+for par in \${!path_pars_files[@]}; do
+    curr_val="\${!par}"
+    file_dir=\$(dirname "\$curr_val")
+    mkdir -p "\$file_dir" && printf "\\t%s\\n" "\$file_dir created."
 done
 
-echo
-echo "Copying nrReadsNrGenesPerChrom files..."
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<\$par_nrReadsNrGenesPerChrom
-for i in "\${nrReadsNrGenesPerChrom[@]}"; do
-  echo "Copying \$i to \$par_nrReadsNrGenesPerChrom_dir/"
-  cp -rL "\$i" "\$par_nrReadsNrGenesPerChrom_dir/"
+echo "Copying output for inputs that are directories"
+for par in \${!path_pars_dirs[@]}; do
+  printf "\\t%s\\n" "Copying output for '\$par'"
+  output_val="\${!par}"
+  input_par_name="\${path_pars_dirs[\${par}]}"
+  input_val="\${!input_par_name}"
+  IFS=";" read -ra output_files_list <<<\$input_val
+  for i in "\${output_files_list[@]}"; do 
+      printf "\\t%s\\n" "Copying '\$i' to '\$output_val'" 
+      cp -a --keep-directory-symlink "\$i" "\$output_val/"
+  done
 done
 
-echo
-echo "Copying STAR QC metrics files..."
-IFS=";" read -ra star_qc_metrics <<<\$par_star_qc_metrics
-for i in "\${star_qc_metrics[@]}"; do
-  echo "Copying \$i to \$par_star_qc_metrics_dir/"
-  cp -rL "\$i" "\$par_star_qc_metrics_dir/"
-done
-
-echo
-echo "Copying eset files..."
-IFS=";" read -ra eset <<<\$par_eset
-for i in "\${eset[@]}"; do
-  echo "Copying \$i to \$par_eset_dir/"
-  cp -rL "\$i" "\$par_eset_dir/"
-done
-
-echo
-echo "Copying f_data files..."
-IFS=";" read -ra f_data <<<\$par_f_data
-for i in "\${f_data[@]}"; do
-  echo "Copying \$i to \$par_f_data_dir/"
-  cp -rL "\$i" "\$par_f_data_dir/"
-done
-
-echo
-echo "Copying p_data files..."
-IFS=";" read -ra p_data <<<\$par_p_data
-for i in "\${p_data[@]}"; do
-  echo "Copying \$i to \$par_p_data_dir/"
-  cp -rL "\$i" "\$par_p_data_dir/"
-done
-
-echo
 echo "Copying single files directly..."
-mkdir -p \$(dirname "\$par_html_report_output")
-echo "Copying \$par_html_report to \$par_html_report_output"
-cp -L "\$par_html_report" "\$par_html_report_output"
+for par in \${!path_pars_files[@]}; do
+  output_val="\${!par}"
+  input_par_name="\${path_pars_files[\${par}]}"
+  input_val="\${!input_par_name}"
+  cp -a --keep-directory-symlink "\$input_val" "\$output_val"
+done
 
-echo "Copying \$par_run_params to \$par_run_params_output"
-mkdir -p \$(dirname "\$par_run_params_output")
-cp -L "\$par_run_params" "\$par_run_params_output"
-
-echo
 echo "Publishing completed successfully!"
 VIASHMAIN
 bash "\$tempscript" &
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index d3380c78..44f88111 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -285,7 +285,7 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index ffdfdd7b..a41138b5 100755
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index cd1f5ca8..98574f76 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index 24b60e47..fc49d97b 100755
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:10Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index 18a2c32d..531b3bd2 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -204,7 +204,7 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index 4a1d9a2d..daf3b8e5 100755
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index 3de10c57..37bb8617 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index df3bbd04..558166a4 100755
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:12Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index c8b479fb..8db4c17d 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -260,7 +260,7 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index a712382c..3445ac56 100755
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:10Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml
index 63bbf7e6..953c90d4 100644
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -151,7 +151,7 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params
index 2de5708d..40c8a879 100755
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "pyyaml"
 
 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-09-10T19:03:11Z"
+LABEL org.opencontainers.image.created="2025-09-23T11:13:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+LABEL org.opencontainers.image.revision="5d5edb788838401c29a4de50b74bb75d5bce6b98"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index f6d1b46f..a4045d5a 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index 3bd05847..35022462 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,7 +3309,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index c828538a..8cd9d6a2 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index 8eb09740..172ebb37 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index 886aeca6..91deb12c 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index adeab065..c3638ff7 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,7 +3293,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 63ec9138..1479f900 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,7 +155,7 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
index 095079ca..264c328f 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,7 +3233,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index 42f1890e..c2bb5aff 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -164,7 +164,7 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
index 14a52e8d..1d2ddeb7 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3244,7 +3244,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
index ff3ec0b2..dd813a03 100644
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -139,7 +139,7 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf
index 84103a5b..c2416697 100644
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,7 +3207,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3298,7 +3298,7 @@ echo "Copying files..."
 IFS=";" read -ra input <<<\\$par_input
 
 for i in "\\${input[@]}"; do
-  cp -rL "\\$i" "\\$par_output/"
+  cp -a --keep-directory-symlink "\\$i" "\\$par_output/"
 done
 VIASHMAIN
 bash "$tempscript"
diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml
index 126660b4..59ec63e7 100644
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf
index a431b78d..ecc16be6 100644
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3369,7 +3369,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3470,89 +3470,62 @@ echo "Publishing results to multiple output directories"
 # Create output directories for multiple files
 echo "Creating output directories..."
 
-path_pars=(
-  par_star_output_dir
-  par_nrReadsNrGenesPerChrom_dir
-  par_star_qc_metrics_dir
-  par_eset_dir
-  par_f_data_dir
-  par_p_data_dir
-  par_html_report_output
-  par_run_params_output
+declare -A path_pars_dirs=(
+  ["par_star_output_dir"]="par_star_output"
+  ["par_nrReadsNrGenesPerChrom_dir"]="par_nrReadsNrGenesPerChrom"
+  ["par_star_qc_metrics_dir"]="par_star_qc_metrics"
+  ["par_eset_dir"]="par_eset"
+  ["par_f_data_dir"]="par_f_data"
+  ["par_p_data_dir"]="par_p_data"
 )
 
-for par in \\${path_pars[@]}; do
+declare -A path_pars_files=(
+  ["par_html_report_output"]="par_html_report"
+  ["par_run_params_output"]="par_run_params"
+)
+
+echo "Canonicalizing output paths."
+all_path_args=( "\\${!path_pars_files[@]}" "\\${!path_pars_dirs[@]}" )
+for par in \\${all_path_args[@]}; do
     curr_val="\\${!par}"
+    printf "\\\\t%s\\\\n" "Canonicalizing path '\\$curr_val'"
     new_value=\\$(realpath --canonicalize-missing "\\$curr_val")
+    printf "\\\\t%s\\\\n" "New output path for '\\$par': '\\$new_value'"
     declare -g "\\$par=\\$new_value"
 done
 
-mkdir -p "\\$par_star_output_dir" && echo "\\$par_star_output_dir created"
-mkdir -p "\\$par_nrReadsNrGenesPerChrom_dir" && echo "\\$par_nrReadsNrGenesPerChrom_dir created"  
-mkdir -p "\\$par_star_qc_metrics_dir" && echo "\\$par_star_qc_metrics_dir created"
-mkdir -p "\\$par_eset_dir" && echo "\\$par_eset_dir created"
-mkdir -p "\\$par_f_data_dir" && echo "\\$par_f_data_dir created"
-mkdir -p "\\$par_p_data_dir" && echo "\\$par_p_data_dir created"
-
-echo
-echo "Copying STAR output files..."
-IFS=";" read -ra star_output <<<\\$par_star_output
-for i in "\\${star_output[@]}"; do
-  echo "Copying \\$i to \\$par_star_output_dir/"
-  cp -rL "\\$i" "\\$par_star_output_dir/"
+echo "Creating output directories"
+for par in \\${!path_pars_dirs[@]}; do
+    curr_val="\\${!par}"
+    mkdir -p "\\$curr_val" && printf "\\\\t%s\\\\n" "\\$curr_val created."
+done
+for par in \\${!path_pars_files[@]}; do
+    curr_val="\\${!par}"
+    file_dir=\\$(dirname "\\$curr_val")
+    mkdir -p "\\$file_dir" && printf "\\\\t%s\\\\n" "\\$file_dir created."
 done
 
-echo
-echo "Copying nrReadsNrGenesPerChrom files..."
-IFS=";" read -ra nrReadsNrGenesPerChrom <<<\\$par_nrReadsNrGenesPerChrom
-for i in "\\${nrReadsNrGenesPerChrom[@]}"; do
-  echo "Copying \\$i to \\$par_nrReadsNrGenesPerChrom_dir/"
-  cp -rL "\\$i" "\\$par_nrReadsNrGenesPerChrom_dir/"
+echo "Copying output for inputs that are directories"
+for par in \\${!path_pars_dirs[@]}; do
+  printf "\\\\t%s\\\\n" "Copying output for '\\$par'"
+  output_val="\\${!par}"
+  input_par_name="\\${path_pars_dirs[\\${par}]}"
+  input_val="\\${!input_par_name}"
+  IFS=";" read -ra output_files_list <<<\\$input_val
+  for i in "\\${output_files_list[@]}"; do 
+      printf "\\\\t%s\\\\n" "Copying '\\$i' to '\\$output_val'" 
+      cp -a --keep-directory-symlink "\\$i" "\\$output_val/"
+  done
 done
 
-echo
-echo "Copying STAR QC metrics files..."
-IFS=";" read -ra star_qc_metrics <<<\\$par_star_qc_metrics
-for i in "\\${star_qc_metrics[@]}"; do
-  echo "Copying \\$i to \\$par_star_qc_metrics_dir/"
-  cp -rL "\\$i" "\\$par_star_qc_metrics_dir/"
-done
-
-echo
-echo "Copying eset files..."
-IFS=";" read -ra eset <<<\\$par_eset
-for i in "\\${eset[@]}"; do
-  echo "Copying \\$i to \\$par_eset_dir/"
-  cp -rL "\\$i" "\\$par_eset_dir/"
-done
-
-echo
-echo "Copying f_data files..."
-IFS=";" read -ra f_data <<<\\$par_f_data
-for i in "\\${f_data[@]}"; do
-  echo "Copying \\$i to \\$par_f_data_dir/"
-  cp -rL "\\$i" "\\$par_f_data_dir/"
-done
-
-echo
-echo "Copying p_data files..."
-IFS=";" read -ra p_data <<<\\$par_p_data
-for i in "\\${p_data[@]}"; do
-  echo "Copying \\$i to \\$par_p_data_dir/"
-  cp -rL "\\$i" "\\$par_p_data_dir/"
-done
-
-echo
 echo "Copying single files directly..."
-mkdir -p \\$(dirname "\\$par_html_report_output")
-echo "Copying \\$par_html_report to \\$par_html_report_output"
-cp -L "\\$par_html_report" "\\$par_html_report_output"
+for par in \\${!path_pars_files[@]}; do
+  output_val="\\${!par}"
+  input_par_name="\\${path_pars_files[\\${par}]}"
+  input_val="\\${!input_par_name}"
+  cp -a --keep-directory-symlink "\\$input_val" "\\$output_val"
+done
 
-echo "Copying \\$par_run_params to \\$par_run_params_output"
-mkdir -p \\$(dirname "\\$par_run_params_output")
-cp -L "\\$par_run_params" "\\$par_run_params_output"
-
-echo
 echo "Publishing completed successfully!"
 VIASHMAIN
 bash "$tempscript"
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index 736be1a4..0cb19470 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -285,7 +285,7 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index 0c4f0cd5..aff27a97 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,7 +3379,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index 80678641..6caa0a44 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index 046147a6..f607d287 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3323,7 +3323,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index a751fac5..1fceca29 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -204,7 +204,7 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index 9b91eef3..7e620acf 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,7 +3295,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index a613bd57..3c25a0b2 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index 4ec8c080..59cea4fe 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index 4f999237..413e21db 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -260,7 +260,7 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index ac597549..9aad60cd 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3361,7 +3361,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml
index 9922185f..873de6e1 100644
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -160,7 +160,7 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.3.0/nextflow/concat_text"
diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf
index ff41fcd9..1b8e69bc 100644
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,7 +3229,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml
index 5d811cac..76799155 100644
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -169,7 +169,7 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf
index 38d9e7c1..7cce94be 100644
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3236,7 +3236,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml
index 519c6d76..a033b705 100644
--- a/target/nextflow/utils/save_params/.config.vsh.yaml
+++ b/target/nextflow/utils/save_params/.config.vsh.yaml
@@ -151,7 +151,7 @@ build_info:
   output: "target/nextflow/utils/save_params"
   executable: "target/nextflow/utils/save_params/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf
index 9fe5a76c..0f9e93b2 100644
--- a/target/nextflow/utils/save_params/main.nf
+++ b/target/nextflow/utils/save_params/main.nf
@@ -3223,7 +3223,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/utils/save_params",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index b6e3c822..32c1bae8 100644
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -345,7 +345,7 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index 11452b55..c44aedc8 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3484,7 +3484,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3694,7 +3694,7 @@ workflow run_wf {
         return [id, new_state]
       } 
       | parallel_map.run(
-        directives: ["label": ["highmem", "lowcpu"]],
+        directives: ["label": ["highmem", "highcpu"]],
         fromState: {id, state ->
           [
             "input_r1": state.input_r1,
diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml
index 72f9fdad..30939c4a 100644
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -322,7 +322,7 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/utils/listInputDir"
diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf
index b238145b..3e2ea02a 100644
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3431,7 +3431,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3491,6 +3491,16 @@ def date = new Date().format('yyyyMMdd_hhmmss')
 def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml")
 def version = get_version(viash_config)
 
+if (!params.containsKey("results_publish_dir") || !params.containsKey("fastq_publish_dir")) {
+   error "Please set both 'results_publish_dir' and 'fastq_publish_dir'."
+}
+
+// S3 paths containing double slashes might cause issues with empty objects being created
+// Remove trailing slashes from the publish dir. The params map is immutable, so create a copy
+def regex_trailing_slashes = ~/\/+$/
+def results_publish_dir = params.results_publish_dir - regex_trailing_slashes
+def fastq_publish_dir = params.fastq_publish_dir - regex_trailing_slashes
+
 workflow run_wf {
   take:
     raw_ch
@@ -3644,7 +3654,7 @@ workflow run_wf {
               assert star_sample_dir.name == state.sample_id: "Unexpected state: the parent directory of STAR output \
                 path '${it}' should match with the sample ID ${sample_id}"
               star_sample_dir
-            }
+            }.unique()
           }
           def new_state = [
             "star_output": star_output_samples,
@@ -3693,7 +3703,7 @@ workflow run_wf {
         fromState: { id, state ->
           def prefix = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
 
-          println("Publising results to ${params.results_publish_dir}/${prefix}")
+          println("Publising results to ${results_publish_dir}/${prefix}")
 
           [ 
             // Inputs
@@ -3719,7 +3729,7 @@ workflow run_wf {
         toState: { id, result, state -> result + ["run_params": state.run_params] },
         directives: [
           publishDir: [
-            path: "${params.results_publish_dir}", 
+            path: results_publish_dir, 
             overwrite: false,
             mode: "copy"
           ]
@@ -3766,7 +3776,7 @@ workflow run_wf {
         toState: { id, result, state -> state },
         directives: [
           publishDir: [
-            path: "${params.fastq_publish_dir}", 
+            path: fastq_publish_dir, 
             overwrite: false,
             mode: "copy"
           ]
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index 740b4906..2ce82009 100644
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index 9a7e7c80..b67e927b 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3327,7 +3327,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
index 89b46039..06eff17c 100644
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/nextflow/workflows/well_metadata"
   executable: "target/nextflow/workflows/well_metadata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "03e7939a9b777dcc00c455ec4809fe76b3aa46da"
+  git_commit: "5d5edb788838401c29a4de50b74bb75d5bce6b98"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf
index 693f0848..c1a5c97b 100644
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,7 +3299,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
     "viash_version" : "0.9.4",
-    "git_commit" : "03e7939a9b777dcc00c455ec4809fe76b3aa46da",
+    "git_commit" : "5d5edb788838401c29a4de50b74bb75d5bce6b98",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {