Build branch main with version main (bd5b2d4)

Build pipeline: viash-hub.htrnaseq.main-l2658 Source commit: bd5b2d4171 Source message: Keep contents for barcodes with no mapped reads. (#44)
2025-02-21 11:49:43 +00:00
parent 6468e4a5de
commit e5a3fd36ee
71 changed files with 340 additions and 125 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,16 @@
+# htrnaseq v0.5.4
+
+* Fix missing barcodes in the output from `generate_pool_statistics`, which caused an assertion error in `create_pdata`.
+  In order to resolve the issue `generate_well_statistics` now outputs results for all chromosomes/scaffolds presented by
+  the genome annotation, even when no reads were mapped to the regions in question. `generate_pool_statistics` will now
+  remove regions from the output that have not at least one counts across all barcodes (PR #44).
+
+# 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
--- 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/stats/generate_pool_statistics/script.py
+++ b/src/stats/generate_pool_statistics/script.py
@@ -1,4 +1,5 @@
 import pandas as pd
+from pathlib import Path
 import re

 ### VIASH START
@@ -16,20 +17,25 @@ if __name__ == "__main__":
    # nrReadsNrGenesPerChrom file
    #########
    nr_reads_nr_genes_wells = []
+    par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"]))
    for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]:
-        nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, 
-                                                   header=0, delimiter="\t",
-                                                   dtype={"WellBC":	pd.StringDtype(),
-                                                          "WellID": pd.StringDtype(),
-                                                          "Chr": pd.StringDtype(),
-                                                          "NumberOfReads": pd.UInt64Dtype(),
-                                                          "NumberOfGenes": pd.UInt64Dtype()}))
+        nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file,
+                                            header=0, delimiter="\t",
+                                            dtype={"WellBC": pd.StringDtype(),
+                                                   "WellID": pd.StringDtype(),
+                                                   "Chr": pd.StringDtype(),
+                                                   "NumberOfReads": pd.UInt64Dtype(),
+                                                   "NumberOfGenes": pd.UInt64Dtype()})
+        if nr_reads_nr_gene_well.empty:
+            raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!")
+        nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well)
    nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,)
    total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr",
                                                                       values=["NumberOfReads"], fill_value=0,
                                                                       aggfunc="sum").droplevel(0, axis=1)
    total_nr_reads_per_chromosome.columns.name = None
-
+    # Remove scaffolds/chromosomes with no counts
+    total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)]
    ##### Total number of genes from all chromosomes
    total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum()

--- a/src/stats/generate_pool_statistics/test.py
+++ b/src/stats/generate_pool_statistics/test.py
@@ -1,8 +1,11 @@
 from uuid import uuid4
 from textwrap import dedent
+from subprocess import CalledProcessError
 import pandas as pd
+import re
 import pytest
 import sys
+from pathlib import Path

 ### VIASH START
 meta = {
@@ -16,7 +19,7 @@ meta = {
 def random_path(tmp_path):
    def wrapper(extension=None):
        extension = "" if not extension else f".{extension}"
-        return tmp_path / f"{uuid4()}{extension}"
+        return Path(tmp_path / f"{uuid4()}{extension}")
    return wrapper


@@ -181,33 +184,77 @@ def test_only_numerical_chromosomes(run_component, random_tsv_path):
    pd.testing.assert_frame_equal(contents, expected_frame, check_like=True)


-@pytest.mark.parametrize("simple_input_file_one,expected", [("", "")],
+@pytest.mark.parametrize("simple_input_file_one", [("")],
                         indirect=["simple_input_file_one"])
-def test_one_empty_input(run_component, simple_input_file_one, expected, empty_input_file, random_tsv_path):
+def test_empty_input_raises(run_component, simple_input_file_one, empty_input_file, random_tsv_path):
+    """
+    When an input file contains no data, raise an error.
+    """
    output_path = random_tsv_path()
+    with pytest.raises(CalledProcessError) as err:
+        run_component([
+            "--nrReadsNrGenesPerChrom", simple_input_file_one,
+            "--nrReadsNrGenesPerChrom", empty_input_file,
+            "--nrReadsNrGenesPerChromPool", output_path
+        ])
+    assert re.search(
+        rf"{empty_input_file.name} does not seem to contain any information",
+        err.value.stdout.decode("utf-8"),
+    )
+
+def test_remove_chromosomes_with_no_counts(run_component, random_tsv_path):
+    """
+    If a chromosome has no counts across all of the wells, it should
+    not be included in the output
+    """
+    output_path = random_tsv_path()
+    contents1 = dedent(
+    f"""\
+    WellBC	WellID	Chr	NumberOfReads	NumberOfGenes
+    CCC	B2	2	2	1
+    CCC	B2	3	3	2
+    CCC	B2	5	4	2
+    CCC	B2	1	4	2
+    CCC	B2	empty	0	0
+    """)
+    input_file_1 = random_tsv_path()
+    with input_file_1.open("w") as open_file:
+        open_file.write(contents1)
+
+    contents2 = dedent(
+    f"""\
+    WellBC	WellID	Chr	NumberOfReads	NumberOfGenes
+    AGG	A1	2	2	1
+    AGG	A1	3	3	2
+    AGG	A1	5	4	2
+    AGG	A1	1	4	2
+    AGG	A1	empty	0	0
+    """)
+    input_file_2 = random_tsv_path()
+    with input_file_2.open("w") as open_file:
+        open_file.write(contents2)
+        output_path = random_tsv_path()
    run_component([
-        "--nrReadsNrGenesPerChrom", simple_input_file_one,
-        "--nrReadsNrGenesPerChrom", empty_input_file,
+        "--nrReadsNrGenesPerChrom", input_file_1,
+        "--nrReadsNrGenesPerChrom", input_file_2,
        "--nrReadsNrGenesPerChromPool", output_path
    ])
+    # Here, the chromosome called "empty" should not be included
    expected_dict = {
-        "WellBC": ["AGG"],
-        "WellID": ["A1"],
-        f"{expected}1": ["2"],
-        f"{expected}2": ["3"],
-        f"{expected}3": ["4"],
-        "ERCC-1": ["1"],
-        "ERCC-2": ["1"],
-        "MT": ["4"],
-        f"{expected}X": ["2"],
-        "pctChrom": ["52.94"],
-        "pctMT": ["23.53"],
-        "pctERCC": ["11.76"],
-        "SumReads": ["17"],
-        "NumberOfGenes": ["12"],
-        "NumberOfERCCReads": ["2"],
-        "NumberOfChromReads": ["9"],
-        "NumberOfMTReads": ["4"],
+        "WellBC": ["AGG", "CCC"],
+        "WellID": ["A1", "B2"],
+        "1": ["4", "4"],
+        "2": ["2", "2"],
+        "3": ["3", "3"],
+        "5": ["4", "4"],
+        "pctChrom": ["100", "100"],
+        "pctMT": ["0", "0"],
+        "pctERCC": ["0", "0"],
+        "SumReads": ["13", "13"],
+        "NumberOfGenes": ["7", "7"],
+        "NumberOfERCCReads": ["0", "0"],
+        "NumberOfChromReads": ["13", "13"],
+        "NumberOfMTReads": ["0", "0"],
    }
    expected_frame = pd.DataFrame.from_dict(expected_dict,
                                            dtype=pd.StringDtype())
--- a/src/stats/generate_well_statistics/script.py
+++ b/src/stats/generate_well_statistics/script.py
@@ -53,6 +53,7 @@ if __name__ == "__main__":
        NumberOfReads=pd.NamedAgg("GX", aggfunc="size"),
        NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique")
    )
+    nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0)
    logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s",
                par['nrReadsNrGenesPerChrom'])
    nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\
--- a/src/stats/generate_well_statistics/test.py
+++ b/src/stats/generate_well_statistics/test.py
@@ -114,8 +114,8 @@ def test_generate_well_statistics_simple_bam(run_component, input_sam_path, sam_

 def test_empty_sam(run_component, empty_sam_path, sam_to_bam, random_path):
    """
-    Test an empty bam file
-    Ran into issue https://github.com/pandas-dev/pandas/pull/59258
+    Test an empty bam file. Make sure that chromosomes with mapped reads
+    are still represented. Ran into issue https://github.com/pandas-dev/pandas/pull/59258
    """
    bam_file = sam_to_bam(empty_sam_path)
    processed_bam = random_path("tsv")
@@ -143,6 +143,8 @@ def test_empty_sam(run_component, empty_sam_path, sam_to_bam, random_path):
    expected_reads_per_chromosome = \
    dedent("""\
    WellBC	WellID	Chr	NumberOfReads	NumberOfGenes
+    ACGT	A1	1	0	0
+    ACGT	A1	2	0	0
    """)

    expected_nr_reads_nr_umis_per_cb = \
--- a/src/workflows/htrnaseq/config.vsh.yaml
+++ b/src/workflows/htrnaseq/config.vsh.yaml
@@ -96,6 +96,9 @@ test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf
+  - type: nextflow_script
+    path: test.nf
+    entrypoint: test_wf2
 dependencies:
  - name: stats/combine_star_logs
    repository: local
--- a/src/workflows/htrnaseq/integration_test.sh
+++ b/src/workflows/htrnaseq/integration_test.sh
@@ -11,6 +11,8 @@ viash ns build --setup cb --parallel

 export NXF_VER=24.04.4

+set -eo pipefail
+
 nextflow \
  run . \
  -main-script src/workflows/htrnaseq/test.nf \
@@ -19,3 +21,13 @@ nextflow \
  -resume \
  -profile docker,local \
  --publish_dir output
+
+nextflow \
+  run . \
+  -main-script src/workflows/htrnaseq/test.nf \
+  -config ./src/config/labels.config \
+  -entry test_wf2 \
+  -resume \
+  -profile docker,local \
+  --publish_dir output2
+
--- a/src/workflows/htrnaseq/test.nf
+++ b/src/workflows/htrnaseq/test.nf
@@ -43,3 +43,28 @@ workflow test_wf {
        ]
    )
 }
+
+
+workflow test_wf2 {
+  // Test the edge case where one of the barcodes has no reads
+  resources_test_file = file(params.resources_test)
+  input_ch = Channel.fromList([
+      [
+          id: "sample_one",
+          input_r1: resources_test_file.resolve("100k/SRR14730301/VH02001612_S9_R1_001.fastq"),
+          input_r2: resources_test_file.resolve("100k/SRR14730301/VH02001612_S9_R2_001.fastq"),
+          genomeDir: resources_test_file.resolve("genomeDir/gencode.v41.star.sparse"),
+          barcodesFasta: resources_test_file.resolve("2-wells-1-no-reads.fasta"),
+          annotation: resources_test_file.resolve("genomeDir/gencode.v41.annotation.gtf.gz")
+      ],
+    ])
+    | map{ state -> [state.id, state] }
+    | view { "Input: $it" }
+    | htrnaseq.run(
+        toState: [
+            "eset": "eset",
+            "star_output": "star_output",
+        ]
+    )
+}
+
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -477,9 +477,9 @@ 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="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -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
@@ -177,7 +177,7 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -478,9 +478,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -191,7 +191,7 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -488,9 +488,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,7 +148,7 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -470,9 +470,9 @@ 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="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- 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
@@ -158,7 +158,7 @@ build_info:
  output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- 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
@@ -476,9 +476,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -143,7 +143,7 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -470,9 +470,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:28Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -484,9 +484,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -540,9 +540,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:43Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -476,9 +476,9 @@ 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="2025-02-17T14:58:43Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -198,7 +198,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:28Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,7 +182,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1044,6 +1044,7 @@ trap clean_up EXIT
 trap interrupt INT SIGINT
 cat > "\$tempscript" << 'VIASHMAIN'
 import pandas as pd
+from pathlib import Path
 import re

 ### VIASH START
@@ -1085,20 +1086,25 @@ if __name__ == "__main__":
    # nrReadsNrGenesPerChrom file
    #########
    nr_reads_nr_genes_wells = []
+    par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"]))
    for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]:
-        nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, 
-                                                   header=0, delimiter="\\t",
-                                                   dtype={"WellBC":	pd.StringDtype(),
-                                                          "WellID": pd.StringDtype(),
-                                                          "Chr": pd.StringDtype(),
-                                                          "NumberOfReads": pd.UInt64Dtype(),
-                                                          "NumberOfGenes": pd.UInt64Dtype()}))
+        nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file,
+                                            header=0, delimiter="\\t",
+                                            dtype={"WellBC": pd.StringDtype(),
+                                                   "WellID": pd.StringDtype(),
+                                                   "Chr": pd.StringDtype(),
+                                                   "NumberOfReads": pd.UInt64Dtype(),
+                                                   "NumberOfGenes": pd.UInt64Dtype()})
+        if nr_reads_nr_gene_well.empty:
+            raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!")
+        nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well)
    nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,)
    total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr",
                                                                       values=["NumberOfReads"], fill_value=0,
                                                                       aggfunc="sum").droplevel(0, axis=1)
    total_nr_reads_per_chromosome.columns.name = None
-
+    # Remove scaffolds/chromosomes with no counts
+    total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)]
    ##### Total number of genes from all chromosomes
    total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum()

--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -264,7 +264,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z"
+LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1259,6 +1259,7 @@ if __name__ == "__main__":
        NumberOfReads=pd.NamedAgg("GX", aggfunc="size"),
        NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique")
    )
+    nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0)
    logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s",
                par['nrReadsNrGenesPerChrom'])
    nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\\
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3072,7 +3072,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -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),
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -177,7 +177,7 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -191,7 +191,7 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3058,7 +3058,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,7 +148,7 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -2997,7 +2997,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- 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
@@ -158,7 +158,7 @@ build_info:
  output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- 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
@@ -3009,7 +3009,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -143,7 +143,7 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -2983,7 +2983,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3032,7 +3032,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3144,7 +3144,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3077,7 +3077,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -198,7 +198,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3060,7 +3060,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,7 +182,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3096,6 +3096,7 @@ def innerWorkflowFactory(args) {
 tempscript=".viash_script.sh"
 cat > "$tempscript" << VIASHMAIN
 import pandas as pd
+from pathlib import Path
 import re

 ### VIASH START
@@ -3137,20 +3138,25 @@ if __name__ == "__main__":
    # nrReadsNrGenesPerChrom file
    #########
    nr_reads_nr_genes_wells = []
+    par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"]))
    for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]:
-        nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, 
-                                                   header=0, delimiter="\\\\t",
-                                                   dtype={"WellBC":	pd.StringDtype(),
-                                                          "WellID": pd.StringDtype(),
-                                                          "Chr": pd.StringDtype(),
-                                                          "NumberOfReads": pd.UInt64Dtype(),
-                                                          "NumberOfGenes": pd.UInt64Dtype()}))
+        nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file,
+                                            header=0, delimiter="\\\\t",
+                                            dtype={"WellBC": pd.StringDtype(),
+                                                   "WellID": pd.StringDtype(),
+                                                   "Chr": pd.StringDtype(),
+                                                   "NumberOfReads": pd.UInt64Dtype(),
+                                                   "NumberOfGenes": pd.UInt64Dtype()})
+        if nr_reads_nr_gene_well.empty:
+            raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!")
+        nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well)
    nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,)
    total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr",
                                                                       values=["NumberOfReads"], fill_value=0,
                                                                       aggfunc="sum").droplevel(0, axis=1)
    total_nr_reads_per_chromosome.columns.name = None
-
+    # Remove scaffolds/chromosomes with no counts
+    total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)]
    ##### Total number of genes from all chromosomes
    total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum()

--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -264,7 +264,7 @@ 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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3139,7 +3139,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3270,6 +3270,7 @@ if __name__ == "__main__":
        NumberOfReads=pd.NamedAgg("GX", aggfunc="size"),
        NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique")
    )
+    nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0)
    logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s",
                par['nrReadsNrGenesPerChrom'])
    nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\\\\
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -165,7 +165,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3004,7 +3004,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -197,6 +197,10 @@ test_resources:
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf"
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf2"
 info: null
 status: "enabled"
 requirements:
@@ -319,7 +323,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3049,6 +3049,12 @@ meta = [
      "path" : "test.nf",
      "is_executable" : true,
      "entrypoint" : "test_wf"
+    },
+    {
+      "type" : "nextflow_script",
+      "path" : "test.nf",
+      "is_executable" : true,
+      "entrypoint" : "test_wf2"
    }
  ],
  "status" : "enabled",
@@ -3223,7 +3229,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -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: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/utils/listInputDir"
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3069,7 +3069,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -211,7 +211,7 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3084,7 +3084,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -209,7 +209,7 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
+  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3064,7 +3064,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.0",
-    "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b",
+    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {