Build branch v0.5 with version v0.5.3 (19fced3)

Build pipeline: viash-hub.htrnaseq.v0.5-5lqns Source commit: 19fced3c66 Source message: Bump version to v0.5.3
Build branch v0.5 with version v0.5.2 (4e7d7f7)
2025-02-18 09:22:30 +00:00 · 2025-02-17 15:47:11 +00:00
84 changed files with 520 additions and 364 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,15 @@
+# htrnaseq v0.5.3
+
+## Bug fixes
+
+* Fix `create_eset` component failing to create when one of the input samples has no counts (PR #43).
+
+# htrnaseq v0.5.2
+
+## Bug fixes
+
+* `create_fdata`: remove duplicate entries from feature data (PR #41).
+
 # htrnaseq v0.5.1

 ## Bug fixes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.5.1
+version: v0.5.3
 description: |
  High-throughput pipeline [WIP]
 license: MIT
--- a/src/eset/create_eset/script.R
+++ b/src/eset/create_eset/script.R
@@ -209,7 +209,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
                                output, measure, col_names, cell_barcodes) {

  read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1)
-  read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)]
  # keep index of feature names containing "_" because Seurat
  #changes them to "-" and they no longer match with fdata[, "gene_id"]
  idx <- grep("_", rownames(read_matrix))
@@ -378,7 +377,7 @@ create_eset <- function(feature_annotation_path,
                                  featureData = fdata_eset,
                                  annotation = additional_info)

-
+  eset <- eset[, colSums(exprs(eset)) != 0]
  saveRDS(eset, file = output_path)

  message(paste0("eset created succesfully for ", ncol(eset),
--- a/src/eset/create_eset/test.R
+++ b/src/eset/create_eset/test.R
@@ -73,4 +73,60 @@ input_f_data <- read.table(file.path(meta$resources_dir, "fData.tsv"),
 input_f_data <- input_f_data[input_f_data$gene_id %in% expected_feature_names, ]
 row.names(input_f_data) <- input_f_data$gene_id
 input_f_data[] <- lapply(input_f_data, as.character)
-stopifnot(identical(input_f_data, fData(result)))
+stopifnot(identical(input_f_data, fData(result)))
+
+# Check results filtering of barcodes with no reads
+out <- processx::run(meta$executable, c(
+  "--pDataFile", file.path(meta$resources_dir, "pData.tsv"),
+  "--fDataFile", file.path(meta$resources_dir, "fData.tsv"),
+  "--mappingDir", file.path(meta$resources_dir, "mapping_dir", "AACAAGGTAC"),
+  "--mappingDir", file.path(meta$resources_dir, "mapping_dir", "EMPTY"),
+  "--poolName", "bar",
+  "--output", output
+))
+expect_equal(out$status, 0)
+expect_true(file.exists(output))
+result <- readRDS(output)
+stopifnot(length(sampleNames(result)) == 1)
+stopifnot(all(sampleNames(result) == c("bar_AACAAGGTAC")))
+expected_feature_names <- c(
+    "ENS0001058", "ENS0000221", "ENS0001387", "ENS0000508", "ENS0001199",
+    "ENS0000477", "ENS0001457", "ENS0001040", "ENS0000114", "ENS0000821",
+    "ENS0001429", "ENS0001396", "ENS0000355", "ENS0000122", "ENS0000441",
+    "ENS0001223", "ENS0001431", "ENS0000042", "ENS0000443", "ENS0000389",
+    "ENS0001208", "ENS0001140", "ENS0000071", "ENS0001369"
+)
+stopifnot(length(featureNames(result)) == 24)
+stopifnot(all(featureNames(result) == expected_feature_names))
+expected_expressions <- matrix(
+    c(0,
+      0,
+      0,
+      0,
+      1,
+      0,
+      0,
+      0,
+      2,
+      0,
+      0,
+      8,
+      0,
+      1,
+      2,
+      0,
+      0,
+      0,
+      1,
+      0,
+      16,
+      0,
+      12,
+      5),
+    ncol = 1,
+    nrow = 24,
+    byrow = TRUE,
+)
+rownames(expected_expressions) <- expected_feature_names
+colnames(expected_expressions) <- c("bar_AACAAGGTAC")
+stopifnot(identical(exprs(result), expected_expressions))
--- a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv
+++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv
@@ -0,0 +1 @@
+CCCCCCCCCC
--- a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv
+++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv
@@ -0,0 +1,25 @@
+ENS0001140	209E3	Gene Expression
+ENS0001058	A2B9A	Gene Expression
+ENS0000508	CF168	Gene Expression
+ENS0001457	3BA5A	Gene Expression
+ENS0001431	1C968	Gene Expression
+ENS0000821	E5192	Gene Expression
+ENS0001040	1821B	Gene Expression
+ENS0000443	5AD11	Gene Expression
+ENS0000441	3F0FF	Gene Expression
+ENS0001387	265F2	Gene Expression
+ENS0001223	28A43	Gene Expression
+ENS0001208	58E28	Gene Expression
+ENS0001396	6E614	Gene Expression
+ENS0001199	EA941	Gene Expression
+ENS0001369	99DDC	Gene Expression
+ENS0000770	AFCC0	Gene Expression
+ENS0000389	B58E5	Gene Expression
+ENS0000071	7A6C3	Gene Expression
+ENS0000114	65424	Gene Expression
+ENS0000355	077A2	Gene Expression
+ENS0001429	22A4F	Gene Expression
+ENS0000477	981E6	Gene Expression
+ENS0000042	E2D99	Gene Expression
+ENS0000122	D90E9	Gene Expression
+ENS0000221	97B0F	Gene Expression
--- a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx
+++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx
@@ -0,0 +1,3 @@
+%%MatrixMarket matrix coordinate integer general
+%
+25 1 0
--- a/src/eset/create_fdata/create_fdata.py
+++ b/src/eset/create_fdata/create_fdata.py
@@ -119,10 +119,17 @@ def main(par):
        idx, cols = pd.factorize(column_to_get)
        symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx]
        annotation["SYMBOL"] = symbol_values
-
-    logger.info("Writing to %s", par["output"])
+    logger.info("Dropping unused columns")
    annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1)
+    logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0])
+    annotation = annotation.drop_duplicates(keep="first", ignore_index=True)
+    logger.info("After removing duplicates: %i entries", annotation.shape[0])
+    logger.info("Writing to %s", par["output"])
    annotation.to_csv(par["output"], sep="\t", header=True, index=False, na_rep="NA")
+    # Do these checks *after* writing the csv in order to be able to check the data
+    logger.info("Checking for unique gene IDs")
+    if not annotation["gene_id"].is_unique:
+        raise ValueError("Values from the 'gene_id' column are not unique after processing!") 
    logger.info("%s finished", meta['name'])


--- a/src/eset/create_fdata/test.py
+++ b/src/eset/create_fdata/test.py
@@ -3,6 +3,7 @@ import sys
 import pandas as pd
 from pathlib import Path
 from uuid import uuid4
+from shutil import copyfile

 ### VIASH START
 meta = {
@@ -57,5 +58,45 @@ def test_create_fdata(run_component, test_annotation_path, random_path):
    pd.testing.assert_frame_equal(expected, result, check_like=True)


+def test_make_unique(run_component, test_annotation_path, random_path):
+    gtf_with_duplicate_entry_path = random_path("gtf")
+    output_path = random_path("tsv")
+    entry_to_add = (
+        "\n20	ensembl_havana	gene	87250	97094	.	+	.	gene_id " +
+        "\"ENSG00000178591.7\"; gene_version \"7\"; gene_name \"DEFB125\"; " +
+        "gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\";\n"
+    )
+    copyfile(test_annotation_path, gtf_with_duplicate_entry_path)
+    with gtf_with_duplicate_entry_path.open("a") as open_gtf:
+        open_gtf.write(entry_to_add)
+    run_component([
+        "--gtf", gtf_with_duplicate_entry_path,
+        "--output", output_path
+    ])
+    assert output_path.is_file()
+    result = pd.read_csv(output_path, sep="\t", dtype=pd.StringDtype())
+    expected_dict = {
+        "seqname": ["20", "20", "20", "21"],
+        "start": ["87250", "142590", "157454", "297570"],
+        "end": ["97094", "145751", "159163", "300321"],
+        "strand": ["+", "+", "+", "+"],
+        "gene_id": ["ENSG00000178591", "ENSG00000125788",
+                    "ENSG00000088782", "ENSG00000247315"],
+        "gene_version": ["7", "6", "5", "4"],
+        "gene_name": ["DEFB125", "DEFB126", "DEFB127", pd.NA],
+        "gene_source": ["ensembl_havana", "ensembl_havana",
+                        "ensembl_havana", "havana"],
+        "gene_biotype": ["protein_coding", "protein_coding",
+                         "protein_coding", "protein_coding"],
+        "ENSEMBL_with_version": ["ENSG00000178591.7", "ENSG00000125788",
+                                 "ENSG00000088782", "ENSG00000247315"],
+        "ENSEMBL": ["ENSG00000178591", "ENSG00000125788",
+                    "ENSG00000088782", "ENSG00000247315"],
+        "SYMBOL": ["DEFB125", "DEFB126", "DEFB127", pd.NA]
+    }
+    expected = pd.DataFrame.from_dict(expected_dict, dtype=pd.StringDtype())
+    pd.testing.assert_frame_equal(expected, result, check_like=True)
+
+
 if __name__ == '__main__':
    sys.exit(pytest.main([__file__]))
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -172,7 +172,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -198,11 +198,11 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -217,7 +217,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_eset v0.5.1
+# create_eset v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.5.1"
+  echo "create_eset v0.5.3"
  echo ""
  echo "Arguments:"
  echo "    --pDataFile"
@@ -477,10 +477,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-17T07:53:55Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:19Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_eset v0.5.1"
+            echo "create_eset v0.5.3"
            exit
            ;;
        --pDataFile)
@@ -768,7 +768,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.3'
  fi

  # print dockerfile
@@ -1343,7 +1343,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
                                output, measure, col_names, cell_barcodes) {

  read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1)
-  read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)]
  # keep index of feature names containing "_" because Seurat
  #changes them to "-" and they no longer match with fdata[, "gene_id"]
  idx <- grep("_", rownames(read_matrix))
@@ -1512,7 +1511,7 @@ create_eset <- function(feature_annotation_path,
                                  featureData = fdata_eset,
                                  annotation = additional_info)

-
+  eset <- eset[, colSums(exprs(eset)) != 0]
  saveRDS(eset, file = output_path)

  message(paste0("eset created succesfully for ", ncol(eset),
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -148,7 +148,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -177,11 +177,11 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -196,7 +196,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_fdata v0.5.1
+# create_fdata v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.5.1"
+  echo "create_fdata v0.5.3"
  echo ""
  echo "Create a fdata file"
  echo ""
@@ -478,10 +478,10 @@ 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="2025-02-17T07:53:56Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:19Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -617,7 +617,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_fdata v0.5.1"
+            echo "create_fdata v0.5.3"
            exit
            ;;
        --gtf)
@@ -730,7 +730,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.3'
  fi

  # print dockerfile
@@ -1162,10 +1162,17 @@ def main(par):
        idx, cols = pd.factorize(column_to_get)
        symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx]
        annotation["SYMBOL"] = symbol_values
-
-    logger.info("Writing to %s", par["output"])
+    logger.info("Dropping unused columns")
    annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1)
+    logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0])
+    annotation = annotation.drop_duplicates(keep="first", ignore_index=True)
+    logger.info("After removing duplicates: %i entries", annotation.shape[0])
+    logger.info("Writing to %s", par["output"])
    annotation.to_csv(par["output"], sep="\\t", header=True, index=False, na_rep="NA")
+    # Do these checks *after* writing the csv in order to be able to check the data
+    logger.info("Checking for unique gene IDs")
+    if not annotation["gene_id"].is_unique:
+        raise ValueError("Values from the 'gene_id' column are not unique after processing!") 
    logger.info("%s finished", meta['name'])


--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -162,7 +162,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -191,11 +191,11 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -210,7 +210,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_pdata v0.5.1
+# create_pdata v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.5.1"
+  echo "create_pdata v0.5.3"
  echo ""
  echo "Create a pdata file by combining the mapping statistics"
  echo ""
@@ -488,10 +488,10 @@ 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="2025-02-17T07:53:55Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -627,7 +627,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_pdata v0.5.1"
+            echo "create_pdata v0.5.3"
            exit
            ;;
        --star_stats_file)
@@ -751,7 +751,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -128,7 +128,7 @@ engines:
  id: "docker"
  image: "bioconductor/bioconductor_docker:3.19"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -148,11 +148,11 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -167,7 +167,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_eset v0.5.1
+# check_eset v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.5.1"
+  echo "check_eset v0.5.3"
  echo ""
  echo "This component test the ExpressionSet object as output by the main pipeline."
  echo ""
@@ -470,10 +470,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-17T07:53:55Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:19Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_eset v0.5.1"
+            echo "check_eset v0.5.3"
            exit
            ;;
        --eset)
@@ -728,7 +728,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.3'
  fi

  # print dockerfile
--- 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
@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -135,7 +135,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -158,11 +158,11 @@ 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: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -177,7 +177,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- 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
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# check_cutadapt_output v0.5.1
+# check_cutadapt_output v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_cutadapt_output v0.5.1"
+  echo "check_cutadapt_output v0.5.3"
  echo ""
  echo "This component test the cutadapt output from the well_demultiplex subworkflow."
  echo ""
@@ -476,10 +476,10 @@ 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="2025-02-17T07:53:55Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_cutadapt_output v0.5.1"
+            echo "check_cutadapt_output v0.5.3"
            exit
            ;;
        --fastq_r1)
@@ -757,7 +757,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -125,7 +125,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -143,11 +143,11 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -162,7 +162,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_fastqs v0.5.1
+# publish_fastqs v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.5.1"
+  echo "publish_fastqs v0.5.3"
  echo ""
  echo "Publish the fastq files per well"
  echo ""
@@ -470,10 +470,10 @@ 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="2025-02-17T07:53:54Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_fastqs v0.5.1"
+            echo "publish_fastqs v0.5.3"
            exit
            ;;
        --input_r1)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -187,11 +187,11 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -206,7 +206,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish_results v0.5.1
+# publish_results v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.5.1"
+  echo "publish_results v0.5.3"
  echo ""
  echo "Publish the results"
  echo ""
@@ -484,10 +484,10 @@ 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="2025-02-17T07:53:54Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish_results v0.5.1"
+            echo "publish_results v0.5.3"
            exit
            ;;
        --star_output)
@@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -242,7 +242,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +279,11 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -298,7 +298,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# parallel_map v0.5.1
+# parallel_map v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.5.1"
+  echo "parallel_map v0.5.3"
  echo ""
  echo "Map wells in batch, using STAR"
  echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -540,10 +540,10 @@ 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="2025-02-17T07:53:56Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:19Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -679,7 +679,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "parallel_map v0.5.1"
+            echo "parallel_map v0.5.3"
            exit
            ;;
        --input_r1)
@@ -881,7 +881,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -153,7 +153,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -201,11 +201,11 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -220,7 +220,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# create_report v0.5.1
+# create_report v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.5.1"
+  echo "create_report v0.5.3"
  echo ""
  echo "Create a basic QC report in HTML format based on a number of esets."
  echo ""
@@ -476,10 +476,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-17T07:53:56Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:20Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "create_report v0.5.1"
+            echo "create_report v0.5.3"
            exit
            ;;
        --eset)
@@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -198,11 +198,11 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -217,7 +217,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# combine_star_logs v0.5.1
+# combine_star_logs v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_star_logs v0.5.1"
+  echo "combine_star_logs v0.5.3"
  echo ""
  echo "Arguments:"
  echo "    --barcodes"
@@ -490,10 +490,10 @@ 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="2025-02-17T07:53:54Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "combine_star_logs v0.5.1"
+            echo "combine_star_logs v0.5.3"
            exit
            ;;
        --barcodes)
@@ -799,7 +799,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -153,7 +153,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -182,11 +182,11 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -201,7 +201,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_pool_statistics v0.5.1
+# generate_pool_statistics v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_pool_statistics v0.5.1"
+  echo "generate_pool_statistics v0.5.3"
  echo ""
  echo "Arguments:"
  echo "    --nrReadsNrGenesPerChrom"
@@ -483,10 +483,10 @@ 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="2025-02-17T07:53:54Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_pool_statistics v0.5.1"
+            echo "generate_pool_statistics v0.5.3"
            exit
            ;;
        --nrReadsNrGenesPerChrom)
@@ -741,7 +741,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.3'
  fi

  # print dockerfile
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -224,7 +224,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -264,11 +264,11 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -283,7 +283,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# generate_well_statistics v0.5.1
+# generate_well_statistics v0.5.3
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_well_statistics v0.5.1"
+  echo "generate_well_statistics v0.5.3"
  echo ""
  echo "Generate summary statistics from BAM files generated by STAR solo."
  echo ""
@@ -520,10 +520,10 @@ 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="2025-02-17T07:53:55Z"
+LABEL org.opencontainers.image.created="2025-02-18T08:30:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d"
-LABEL org.opencontainers.image.version="v0.5.1"
+LABEL org.opencontainers.image.revision="19fced3c662da52952181fefe8d3c29a5b1e9e8a"
+LABEL org.opencontainers.image.version="v0.5.3"

 VIASHDOCKER
  fi
@@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "generate_well_statistics v0.5.1"
+            echo "generate_well_statistics v0.5.3"
            exit
            ;;
        --input)
@@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.3'
  fi

  # print dockerfile
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -172,7 +172,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -198,11 +198,11 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -217,7 +217,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -1,4 +1,4 @@
-// create_eset v0.5.1
+// create_eset v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_eset",
  "namespace" : "eset",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3036,7 +3036,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3072,12 +3072,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3094,7 +3094,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3365,7 +3365,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
                                output, measure, col_names, cell_barcodes) {

  read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1)
-  read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)]
  # keep index of feature names containing "_" because Seurat
  #changes them to "-" and they no longer match with fdata[, "gene_id"]
  idx <- grep("_", rownames(read_matrix))
@@ -3534,7 +3533,7 @@ create_eset <- function(feature_annotation_path,
                                  featureData = fdata_eset,
                                  annotation = additional_info)

-
+  eset <- eset[, colSums(exprs(eset)) != 0]
  saveRDS(eset, file = output_path)

  message(paste0("eset created succesfully for ", ncol(eset),
@@ -3947,7 +3946,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_eset/nextflow.config
+++ b/target/nextflow/eset/create_eset/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_eset'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -148,7 +148,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -177,11 +177,11 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -196,7 +196,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -1,4 +1,4 @@
-// create_fdata v0.5.1
+// create_fdata v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_fdata",
  "namespace" : "eset",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3003,7 +3003,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3044,12 +3044,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3066,7 +3066,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3236,10 +3236,17 @@ def main(par):
        idx, cols = pd.factorize(column_to_get)
        symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx]
        annotation["SYMBOL"] = symbol_values
-
-    logger.info("Writing to %s", par["output"])
+    logger.info("Dropping unused columns")
    annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1)
+    logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0])
+    annotation = annotation.drop_duplicates(keep="first", ignore_index=True)
+    logger.info("After removing duplicates: %i entries", annotation.shape[0])
+    logger.info("Writing to %s", par["output"])
    annotation.to_csv(par["output"], sep="\\\\t", header=True, index=False, na_rep="NA")
+    # Do these checks *after* writing the csv in order to be able to check the data
+    logger.info("Checking for unique gene IDs")
+    if not annotation["gene_id"].is_unique:
+        raise ValueError("Values from the 'gene_id' column are not unique after processing!") 
    logger.info("%s finished", meta['name'])


@@ -3606,7 +3613,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_fdata/nextflow.config
+++ b/target/nextflow/eset/create_fdata/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_fdata'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Create a fdata file\n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -162,7 +162,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -191,11 +191,11 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -210,7 +210,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -1,4 +1,4 @@
-// create_pdata v0.5.1
+// create_pdata v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_pdata",
  "namespace" : "eset",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3017,7 +3017,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3058,12 +3058,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3080,7 +3080,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3553,7 +3553,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/eset/create_pdata/nextflow.config
+++ b/target/nextflow/eset/create_pdata/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'eset/create_pdata'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Create a pdata file by combining the mapping statistics \n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -128,7 +128,7 @@ engines:
  id: "docker"
  image: "bioconductor/bioconductor_docker:3.19"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "r"
@@ -148,11 +148,11 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -167,7 +167,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -1,4 +1,4 @@
-// check_eset v0.5.1
+// check_eset v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_eset",
  "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -2971,7 +2971,7 @@ meta = [
      "id" : "docker",
      "image" : "bioconductor/bioconductor_docker:3.19",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2997,12 +2997,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3019,7 +3019,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3646,7 +3646,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'integration_test_components/htrnaseq/check_eset'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'This component test the ExpressionSet object as output by the main pipeline.'
  author = 'Dries Schaumont'
 }
--- 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
@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -135,7 +135,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -158,11 +158,11 @@ 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: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -177,7 +177,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- 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
@@ -1,4 +1,4 @@
-// check_cutadapt_output v0.5.1
+// check_cutadapt_output v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "check_cutadapt_output",
  "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -2978,7 +2978,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3009,12 +3009,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3031,7 +3031,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3527,7 +3527,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
  author = 'Dries Schaumont'
 }
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -125,7 +125,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -143,11 +143,11 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -162,7 +162,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -1,4 +1,4 @@
-// publish_fastqs v0.5.1
+// publish_fastqs v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish_fastqs",
  "namespace" : "io",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2960,7 +2960,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2983,12 +2983,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3005,7 +3005,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3440,7 +3440,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish_fastqs/nextflow.config
+++ b/target/nextflow/io/publish_fastqs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish_fastqs'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Publish the fastq files per well'
 }

--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -187,11 +187,11 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -206,7 +206,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -1,4 +1,4 @@
-// publish_results v0.5.1
+// publish_results v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish_results",
  "namespace" : "io",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3009,7 +3009,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3032,12 +3032,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3054,7 +3054,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3516,7 +3516,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish_results/nextflow.config
+++ b/target/nextflow/io/publish_results/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish_results'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Publish the results'
 }

--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -242,7 +242,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -279,11 +279,11 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -298,7 +298,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -1,4 +1,4 @@
-// parallel_map v0.5.1
+// parallel_map v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "parallel_map",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3097,7 +3097,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3144,12 +3144,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3166,7 +3166,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3911,7 +3911,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/parallel_map/nextflow.config
+++ b/target/nextflow/parallel_map/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'parallel_map'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n'
  author = 'Dries Schaumont, Toni Verbeiren'
 }
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -153,7 +153,7 @@ engines:
  id: "docker"
  image: "rocker/r2u:24.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -201,11 +201,11 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -220,7 +220,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -1,4 +1,4 @@
-// create_report v0.5.1
+// create_report v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "create_report",
  "namespace" : "report",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3016,7 +3016,7 @@ meta = [
      "id" : "docker",
      "image" : "rocker/r2u:24.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3077,12 +3077,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3099,7 +3099,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3561,7 +3561,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/report/create_report/nextflow.config
+++ b/target/nextflow/report/create_report/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'report/create_report'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Create a basic QC report in HTML format based on a number of esets.\n'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -198,11 +198,11 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -217,7 +217,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -1,4 +1,4 @@
-// combine_star_logs v0.5.1
+// combine_star_logs v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_star_logs",
  "namespace" : "stats",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3019,7 +3019,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3060,12 +3060,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3082,7 +3082,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3718,7 +3718,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/combine_star_logs/nextflow.config
+++ b/target/nextflow/stats/combine_star_logs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/combine_star_logs'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  author = 'Dries Schaumont'
 }

--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -153,7 +153,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -182,11 +182,11 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -201,7 +201,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -1,4 +1,4 @@
-// generate_pool_statistics v0.5.1
+// generate_pool_statistics v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "generate_pool_statistics",
  "namespace" : "stats",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3003,7 +3003,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3044,12 +3044,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3066,7 +3066,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3567,7 +3567,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/generate_pool_statistics",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/generate_pool_statistics/nextflow.config
+++ b/target/nextflow/stats/generate_pool_statistics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/generate_pool_statistics'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -224,7 +224,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.5.1"
+  target_tag: "v0.5.3"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -264,11 +264,11 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -283,7 +283,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -1,4 +1,4 @@
-// generate_well_statistics v0.5.1
+// generate_well_statistics v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "generate_well_statistics",
  "namespace" : "stats",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3084,7 +3084,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.5.1",
+      "target_tag" : "v0.5.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3139,12 +3139,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3161,7 +3161,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3658,7 +3658,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/htrnaseq/stats/generate_well_statistics",
-    "tag" : "v0.5.1"
+    "tag" : "v0.5.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/stats/generate_well_statistics/nextflow.config
+++ b/target/nextflow/stats/generate_well_statistics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'stats/generate_well_statistics'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Generate summary statistics from BAM files generated by STAR solo.'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Arguments"
  arguments:
@@ -165,11 +165,11 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -184,7 +184,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -1,4 +1,4 @@
-// listInputDir v0.5.1
+// listInputDir v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "listInputDir",
  "namespace" : "utils",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3004,12 +3004,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3026,7 +3026,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/utils/listInputDir/nextflow.config
+++ b/target/nextflow/utils/listInputDir/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'utils/listInputDir'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'List the contents of a directory and parse contained fastq files'
 }

--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "htrnaseq"
 namespace: "workflows"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -319,7 +319,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
@@ -334,7 +334,7 @@ build_info:
  - "target/nextflow/report/create_report"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -349,7 +349,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -1,4 +1,4 @@
-// htrnaseq v0.5.1
+// htrnaseq v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "htrnaseq",
  "namespace" : "workflows",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3223,12 +3223,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3245,7 +3245,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/workflows/htrnaseq/nextflow.config
+++ b/target/nextflow/workflows/htrnaseq/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'workflows/htrnaseq'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  author = 'Dries Schaumont'
 }

--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "runner"
 namespace: "workflows"
-version: "v0.5.1"
+version: "v0.5.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -207,7 +207,7 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/utils/listInputDir"
@@ -216,7 +216,7 @@ build_info:
  - "target/nextflow/io/publish_results"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -231,7 +231,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.5.1
+// runner v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "runner",
  "namespace" : "workflows",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3069,12 +3069,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3091,7 +3091,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/workflows/runner/nextflow.config
+++ b/target/nextflow/workflows/runner/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'workflows/runner'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Runner for HT RNA-seq pipeline'
 }

--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "well_demultiplex"
 namespace: "workflows"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -211,14 +211,14 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -233,7 +233,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -1,4 +1,4 @@
-// well_demultiplex v0.5.1
+// well_demultiplex v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "well_demultiplex",
  "namespace" : "workflows",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3084,12 +3084,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3106,7 +3106,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/workflows/well_demultiplex/nextflow.config
+++ b/target/nextflow/workflows/well_demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'workflows/well_demultiplex'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  description = 'Demultiplexing on well level'
  author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "well_metadata"
 namespace: "workflows"
-version: "v0.5.1"
+version: "v0.5.3"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -209,11 +209,11 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d"
+  git_commit: "19fced3c662da52952181fefe8d3c29a5b1e9e8a"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
-  version: "v0.5.1"
+  version: "v0.5.3"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
@@ -228,7 +228,7 @@ package_config:
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -1,4 +1,4 @@
-// well_metadata v0.5.1
+// well_metadata v0.5.3
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "well_metadata",
  "namespace" : "workflows",
-  "version" : "v0.5.1",
+  "version" : "v0.5.3",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3064,12 +3064,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.0",
-    "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d",
+    "git_commit" : "19fced3c662da52952181fefe8d3c29a5b1e9e8a",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
-    "version" : "v0.5.1",
+    "version" : "v0.5.3",
    "description" : "High-throughput pipeline [WIP]\n",
    "info" : {
      "test_resources" : [
@@ -3086,7 +3086,7 @@ meta = [
      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.5.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.5.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/workflows/well_metadata/nextflow.config
+++ b/target/nextflow/workflows/well_metadata/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'workflows/well_metadata'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.5.1'
+  version = 'v0.5.3'
  author = 'Dries Schaumont'
 }