diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml
new file mode 100644
index 000000000000..24b202222e35
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tximeta_tximport"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bioconductor-tximeta=1.20.1"
diff --git a/modules/nf-core/tximeta/tximport/main.nf b/modules/nf-core/tximeta/tximport/main.nf
new file mode 100644
index 000000000000..1f7aec3986e3
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/main.nf
@@ -0,0 +1,48 @@
+process TXIMETA_TXIMPORT {
+    label "process_medium"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_0' :
+        'biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path("quants/*")
+    tuple val(meta2), path(tx2gene)
+    tuple val(meta3), path(coldata)
+    val quant_type
+
+    output:
+    tuple val(meta), path("*gene_tpm.tsv")                 , emit: tpm_gene
+    tuple val(meta), path("*gene_counts.tsv")              , emit: counts_gene
+    tuple val(meta), path("*gene_counts_length_scaled.tsv"), emit: counts_gene_length_scaled
+    tuple val(meta), path("*gene_counts_scaled.tsv")       , emit: counts_gene_scaled
+    tuple val(meta), path("*gene_lengths.tsv")             , emit: lengths_gene
+    tuple val(meta), path("*transcript_tpm.tsv")           , emit: tpm_transcript
+    tuple val(meta), path("*transcript_counts.tsv")        , emit: counts_transcript
+    tuple val(meta), path("*transcript_lengths.tsv")       , emit: lengths_transcript
+    path "versions.yml"                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'tximport.r'
+
+    stub:
+    """
+    touch ${meta.id}.gene_tpm.tsv
+    touch ${meta.id}.gene_counts.tsv
+    touch ${meta.id}.gene_counts_length_scaled.tsv
+    touch ${meta.id}.gene_counts_scaled.tsv
+    touch ${meta.id}.gene_lengths.tsv
+    touch ${meta.id}.transcript_tpm.tsv
+    touch ${meta.id}.transcript_counts.tsv
+    touch ${meta.id}.transcript_lengths.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml
new file mode 100644
index 000000000000..8b7b632bdcf1
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/meta.yml
@@ -0,0 +1,120 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "tximeta_tximport"
+description: |
+  Import transcript-level abundances and estimated counts for gene-level
+  analysis packages
+keywords:
+  - gene
+  - kallisto
+  - pseudoalignment
+  - salmon
+  - transcript
+tools:
+  - "tximeta":
+      description: "Transcript Quantification Import with Automatic Metadata"
+      homepage: "https://bioconductor.org/packages/release/bioc/html/tximeta.html"
+      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html"
+      tool_dev_url: "https://github.com/thelovelab/tximeta"
+      doi: "10.1371/journal.pcbi.1007664"
+      licence: ["GPL-2"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - quants:
+      type: directory
+      description: Paths to subdirectories corresponding to
+        sample-wise runs of Salmon or Kallisto
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information related to the species
+        reference e.g. `[ id:'yeast' ]`
+  - tx2gene:
+      type: file
+      description: A transcript to gene mapping table such as those generated
+        by custom/tx2gene
+      pattern: "*.{csv,tsv}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - coldata:
+      type: file
+      description: |
+        Optional 'coldata' file equivalent to a sample sheet where the first
+        column corresponds to the sample names (directory names in the input
+        salmon/ kallisto results)
+      pattern: "*.{csv,tsv}"
+  - quant_type:
+      type: string
+      description: Quantification type, 'kallisto' or 'salmon'
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing information related to the experiment as a whole
+        e.g. `[ id:'SRP123456' ]`
+  - tpm_gene:
+      type: file
+      description: |
+        Abundance (TPM) values derived from tximport output after
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*gene_tpm.tsv"
+  - counts_gene:
+      type: file
+      description: |
+        Count values derived from tximport output after
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*gene_counts.tsv"
+  - counts_gene_length_scaled:
+      type: file
+      description: |
+        Count values derived from tximport output after summarizeToGene(), with
+        a 'countsFromAbundance' specification of 'lengthScaledTPM'
+      pattern: "*gene_counts_length_scaled.tsv"
+  - counts_gene_scaled:
+      type: file
+      description: |
+        Count values derived from tximport output after summarizeToGene(), with
+        a 'countsFromAbundance' specification of 'scaledTPM'
+      pattern: "*gene_counts_scaled.tsv"
+  - gene_lengths:
+      type: file
+      description: |
+        Length values derived from tximport output after summarizeToGene(),
+        without a 'countsFromAbundance' specification
+      pattern: "*gene_lengths.tsv"
+  - tpm_transcript:
+      type: file
+      description: |
+        Abundance (TPM) values derived from tximport output without
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*transcript_tpm.tsv"
+  - counts_transcript:
+      type: file
+      description: |
+        Count values derived from tximport output without
+        summarizeToGene(), without a 'countsFromAbundance' specification
+      pattern: "*transcript_counts.tsv"
+  - transcript_lengths:
+      type: file
+      description: |
+        Length values derived from tximport output without summarizeToGene(),
+        without a 'countsFromAbundance' specification
+      pattern: "*gene_lengths.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@pinin4fjords"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
new file mode 100755
index 000000000000..e255017f8783
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -0,0 +1,227 @@
+#!/usr/bin/env Rscript
+
+# Script for importing and processing transcript-level quantifications.
+# Written by Lorena Pantano, later modified by Jonathan Manning, and released
+# under the MIT license.
+
+# Loading required libraries
+library(SummarizedExperiment)
+library(tximport)
+
+################################################
+################################################
+## Functions                                  ##
+################################################
+################################################
+
+#' Build a table from a SummarizedExperiment object
+#'
+#' This function takes a SummarizedExperiment object and a specific slot name to extract
+#' assay data. It then combines the first two columns of the rowData with the specified
+#' assay data slot into a new data table.
+#'
+#' @param se.obj A SummarizedExperiment object from which to build the table.
+#' @param slot The name of the slot in the assays list from which to extract data.
+#'
+#' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot.
+
+build_table <- function(se.obj, slot) {
+    cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]])
+}
+
+#' Write a table to a file from a SummarizedExperiment object with given parameters
+#'
+#' This function generates a table from a SummarizedExperiment object using specified parameters
+#' and writes the resulting table to a file. The file name is constructed using a prefix and a
+#' suffix from the parameters, and the table is written with tab separation, without quoting text,
+#' and without row names.
+#'
+#' @param params A list containing the parameters needed for file generation and table writing.
+#' The list should include:
+#' - `obj`: A SummarizedExperiment object from which to build the table.
+#' - `slot`: The name of the slot in the assays list from which to extract data.
+#' - `suffix`: Suffix to use for generating the file name.
+#'
+#' @return NULL The function is called for its side effect of writing a file and does not return anything.
+
+write_se_table <- function(params, prefix) {
+    file_name <- paste0(prefix, ".", params\$suffix)
+    write.table(build_table(params\$obj, params\$slot), file_name,
+                sep="\t", quote=FALSE, row.names = FALSE)
+}
+
+#' Read Transcript Metadata from a Given Path
+#'
+#' This function reads transcript metadata from a specified file path. The file is expected to
+#' be a tab-separated values file without headers, containing transcript information. The function
+#' checks if the file is empty and stops execution with an error message if so. It reads the file
+#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional
+#' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`),
+#' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`.
+#'
+#' @param tinfo_path The file path to the transcript information file.
+#'
+#' @return A list containing three elements:
+#' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs.
+#' - `gene`: A data frame with unique gene IDs and gene names.
+#' - `tx2gene`: A data frame mapping transcript IDs to gene IDs.
+
+read_transcript_info <- function(tinfo_path){
+    info <- file.info(tinfo_path)
+    if (info\$size == 0) {
+        stop("tx2gene file is empty")
+    }
+
+    transcript_info <- read.csv(tinfo_path, sep="\t", header = FALSE,
+                                col.names = c("tx", "gene_id", "gene_name"))
+
+    extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]]))
+    transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra))
+    transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ]
+    rownames(transcript_info) <- transcript_info[["tx"]]
+
+    list(transcript = transcript_info,
+        gene = unique(transcript_info[,2:3]),
+        tx2gene = transcript_info[,1:2])
+}
+
+#' Create a SummarizedExperiment Object
+#'
+#' Constructs a SummarizedExperiment object using provided matrices for counts, abundance, and length,
+#' along with metadata for columns and rows. This function facilitates the organization of experimental
+#' data (e.g., RNA-seq or other high-throughput data) in a structured format that is convenient for
+#' further analyses and visualization.
+#'
+#' @param counts A matrix or DataFrame containing counts data, with rows as features (e.g., genes) and
+#' columns as samples.
+#' @param abundance A matrix or DataFrame containing abundance data (e.g., TPM or FPKM) with the same
+#' dimensions and row/column names as the counts data.
+#' @param length A matrix or DataFrame containing feature lengths, matching the dimensions and row/column
+#' names of the counts data.
+#' @param col_data A DataFrame containing sample-level metadata, with rows corresponding to columns in the
+#' counts, abundance, and length matrices.
+#' @param row_data A DataFrame containing feature-level metadata, with rows corresponding to features in
+#' the counts, abundance, and length matrices.
+#'
+#' @return A SummarizedExperiment object containing the supplied data and metadata.
+
+create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) {
+    SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length),
+        colData = col_data,
+        rowData = row_data)
+}
+
+################################################
+################################################
+## Main script starts here                    ##
+################################################
+################################################
+
+# Define pattern for file names based on quantification type
+pattern <- ifelse('$quant_type' == "kallisto", "abundance.tsv", "quant.sf")
+fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T)
+names <- basename(dirname(fns))
+names(fns) <- names
+dropInfReps <- '$quant_type' == "kallisto"
+
+# Import transcript-level quantifications
+txi <- tximport(fns, type = '$quant_type', txOut = TRUE, dropInfReps = dropInfReps)
+
+# Read transcript and sample data
+transcript_info <- read_transcript_info('$tx2gene')
+
+if (file.exists('$coldata')) {
+    coldata <- read.csv('$coldata', sep="\t")
+    coldata <- coldata[match(names, coldata[,1]),]
+    coldata <- cbind(files = fns, coldata)
+} else {
+    message("ColData not available: ", '$coldata')
+    coldata <- data.frame(files = fns, names = names)
+}
+rownames(coldata) <- coldata[["names"]]
+
+# Create initial SummarizedExperiment object
+se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]],
+    DataFrame(coldata), transcript_info\$transcript)
+
+# Setting parameters for writing tables
+params <- list(
+    list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"),
+    list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"),
+    list(obj = se, slot = "length", suffix = "transcript_lengths.tsv")
+)
+
+# Process gene-level data if tx2gene mapping is available
+if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) {
+    tx2gene <- transcript_info\$tx2gene
+    gi <- summarizeToGene(txi, tx2gene = tx2gene)
+    gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM")
+    gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM")
+
+    gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),]
+    rownames(gene_info) <- gene_info[["tx"]]
+
+    col_data_frame <- DataFrame(coldata)
+
+    # Create gene-level SummarizedExperiment objects
+    gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]],
+        col_data_frame, gene_info)
+    gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]],
+        col_data_frame, gene_info)
+    gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]],
+        col_data_frame, gene_info)
+
+    params <- c(params, list(
+        list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"),
+        list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"),
+        list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"),
+        list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"),
+        list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"),
+        list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"),
+        list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv")
+    ))
+}
+
+# Writing tables for each set of parameters
+
+prefix <- ''
+if ('$task.ext.prefix' != 'null'){
+    prefix = '$task.ext.prefix'
+} else if ('$meta.id' != 'null'){
+    prefix = '$meta.id'
+}
+
+done <- lapply(params, write_se_table, prefix)
+
+################################################
+################################################
+## R SESSION INFO                             ##
+################################################
+################################################
+
+sink(paste(prefix, "R_sessionInfo.log", sep = '.'))
+citation("tximeta")
+print(sessionInfo())
+sink()
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+tximeta.version <- as.character(packageVersion('tximeta'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    r-base:', r.version),
+        paste('    bioconductor-tximeta:', tximeta.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test
new file mode 100644
index 000000000000..27061ec44c40
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test
@@ -0,0 +1,199 @@
+nextflow_process {
+
+    name "Test Process TXIMETA_TXIMPORT"
+    script "../main.nf"
+    process "TXIMETA_TXIMPORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom/tx2gene"
+    tag "tximeta"
+    tag "tximeta/tximport"
+    tag "untar"
+
+    test("saccharomyces_cerevisiae - kallisto - gtf") {
+        
+       setup {
+
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['saccharomyces_cerevisiae']['genome']['kallisto_results'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+            run("CUSTOM_TX2GENE") { 
+                script "../../../custom/tx2gene/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['saccharomyces_cerevisiae']['genome']['genome_gfp_gtf'], checkIfExists: true)
+                    ]
+                    input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                    input[2] = 'kallisto'
+                    input[3] = 'gene_id' 
+                    input[4] = 'gene_name'
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+		input[2] = Channel.of([ [], [] ])
+                input[3] = 'kallisto'
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto') },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto') },
+                { assert snapshot(process.out.versions).match('versions_kallisto') },
+            )
+        }
+
+    }
+    
+    test("saccharomyces_cerevisiae - kallisto - gtf - stub") {
+        
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [], [] ])
+                input[1] = Channel.of([ [], [] ])
+		input[2] = Channel.of([ [], [] ])
+                input[3] = 'kallisto'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto -stub') },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto - stub') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto - stub') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto - stub') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto - stub') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto - stub') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto - stub') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto - stub') },
+                { assert snapshot(process.out.versions).match('versions_kallisto - stub') },
+            )
+        }
+
+    }
+    test("saccharomyces_cerevisiae - salmon - gtf") {
+        
+       setup {
+
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['saccharomyces_cerevisiae']['genome']['salmon_results'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+            run("CUSTOM_TX2GENE") { 
+                script "../../../custom/tx2gene/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['saccharomyces_cerevisiae']['genome']['genome_gfp_gtf'], checkIfExists: true)
+                    ]
+                    input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                    input[2] = 'salmon'
+                    input[3] = 'gene_id' 
+                    input[4] = 'gene_name'
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+		input[2] = Channel.of([ [], [] ])
+                input[3] = 'salmon'
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon') },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_salmon') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon') },
+                { assert snapshot(process.out.versions).match('versions_salmon') },
+            )
+        }
+
+    }
+    
+    test("saccharomyces_cerevisiae - salmon - gtf - stub") {
+        
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [], [] ])
+                input[1] = Channel.of([ [], [] ])
+		input[2] = Channel.of([ [], [] ])
+                input[3] = 'salmon'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon -stub') },
+                { assert snapshot(process.out.counts_gene).match('counts_gene_salmon - stub') },
+                { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon - stub') },
+                { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon - stub') },
+                { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon - stub') },
+                { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon - stub') },
+                { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon - stub') },
+                { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon - stub') },
+                { assert snapshot(process.out.versions).match('versions_salmon - stub') },
+            )
+        }
+
+    }
+}
+
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
new file mode 100644
index 000000000000..11b79dbb6353
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
@@ -0,0 +1,594 @@
+{
+    "tpm_gene_salmon -stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.624950043"
+    },
+    "tpm_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.67112954"
+    },
+    "lengths_gene_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.185576246"
+    },
+    "counts_gene_scaled_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.653958581"
+    },
+    "counts_gene_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.165389568"
+    },
+    "lengths_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.688955249"
+    },
+    "versions_salmon - stub": {
+        "content": [
+            [
+                "versions.yml:md5,721fc5c3bfa6792e8982f2662908b836"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.698863128"
+    },
+    "counts_gene_length_scaled_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,4944841ac711124d29673b6b6ed16ef3"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.767001542"
+    },
+    "lengths_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,db6d8ab9f8e1123d5984fd534b4347dc"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.710229136"
+    },
+    "counts_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.7960929"
+    },
+    "tpm_gene_kallisto -stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.155684508"
+    },
+    "counts_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.207029265"
+    },
+    "counts_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.703693047"
+    },
+    "lengths_gene_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.66270305"
+    },
+    "tpm_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,6076364cc78741a4f8bc8935a045d13d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.66339226"
+    },
+    "tpm_transcript_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,7a334b565e1e865efb1caf615f194ef7"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.697263797"
+    },
+    "lengths_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.80450998"
+    },
+    "counts_gene_length_scaled_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.171915858"
+    },
+    "counts_transcript_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.680037609"
+    },
+    "counts_gene_scaled_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,39d14e361434978b3cadae901a26a028"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.772150052"
+    },
+    "counts_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.67022546"
+    },
+    "versions_salmon": {
+        "content": [
+            [
+                "versions.yml:md5,a6476f297a8e9396f4cfc151cd7f25ed"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.719355986"
+    },
+    "counts_gene_length_scaled_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,5f92a6784f6edc5e3b336c71c3ee7daf"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.676693139"
+    },
+    "tpm_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,85d108269769ae0d841247b9b9ed922d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.748907143"
+    },
+    "lengths_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.217230264"
+    },
+    "lengths_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,db6becdf807fd164a9c63dd1dd916d9c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.778373051"
+    },
+    "counts_gene_scaled_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.177826097"
+    },
+    "tpm_transcript_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.786421751"
+    },
+    "lengths_gene_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,1691ea2677612805cd699265c83024d7"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.690776907"
+    },
+    "counts_gene_length_scaled_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.645938511"
+    },
+    "counts_gene_kallisto": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,e89c28692ea214396b2d4cb702a804c3"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.762000393"
+    },
+    "versions_kallisto": {
+        "content": [
+            [
+                "versions.yml:md5,a6476f297a8e9396f4cfc151cd7f25ed"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:13.812751439"
+    },
+    "counts_gene_salmon - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:57.637020412"
+    },
+    "versions_kallisto - stub": {
+        "content": [
+            [
+                "versions.yml:md5,721fc5c3bfa6792e8982f2662908b836"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.226293343"
+    },
+    "tpm_transcript_kallisto - stub": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:25.195424656"
+    },
+    "counts_gene_scaled_salmon": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,fdfb3d23aaf5d4316d81247ec4664ca0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-08T11:43:45.682361988"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tximeta/tximport/tests/tags.yml b/modules/nf-core/tximeta/tximport/tests/tags.yml
new file mode 100644
index 000000000000..fc96a89e0be6
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/tags.yml
@@ -0,0 +1,2 @@
+tximeta/tximport:
+  - "modules/nf-core/tximeta/tximport/**"
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index cfcdd51f009a..d5efa7e75522 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -627,7 +627,8 @@ params {
         'saccharomyces_cerevisiae' {
             'genome' {
                 genome_gfp_gtf                                 = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf"
-                kallisto_results                               = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
+		kallisto_results                               = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
+                salmon_results                                 = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz"
             }
         }
         'generic' {