diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4265b2a6..c739194c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#380](https://github.com/nf-core/differentialabundance/pull/380)] - Replace local filter_diff_table module with nf-core one, and create nf-tests for tabular_to_gsea_chip. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#382](https://github.com/nf-core/differentialabundance/pull/382)] - Add YAML formatted contrasts file handling. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@TODO](https://github.com/TODO))
+- [[#411](https://github.com/nf-core/differentialabundance/pull/411)] - Replace local tabulartogseachip with nf-core version. ([@nschcolnicov](https://github.com/nschcolnicov), review by [@TODO](https://github.com/TODO))
 
 ### Fixed
 
diff --git a/conf/modules.config b/conf/modules.config
index f84aef02..b18c8b1d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -478,7 +478,7 @@ process {
         ]
     }
 
-    withName: 'TABULAR_TO_GSEA_CHIP' {
+    withName: 'CUSTOM_TABULARTOGSEACHIP' {
         publishDir = [
             enabled: false
         ]
diff --git a/modules.json b/modules.json
index 23d47cc3..f46a3b1f 100644
--- a/modules.json
+++ b/modules.json
@@ -25,6 +25,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "custom/tabulartogseachip": {
+                        "branch": "master",
+                        "git_sha": "7900e49fb84969a2479ecfbeef7bcbe296513c90",
+                        "installed_by": ["modules"]
+                    },
                     "custom/tabulartogseacls": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/local/tabulartogseachip/main.nf b/modules/local/tabulartogseachip/main.nf
deleted file mode 100644
index 314a2e70..00000000
--- a/modules/local/tabulartogseachip/main.nf
+++ /dev/null
@@ -1,54 +0,0 @@
-process TABULAR_TO_GSEA_CHIP {
-
-    tag "$id"
-    label 'process_single'
-
-    conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/gawk:5.1.0--fa97c4ccf4cfbc4b"
-
-    input:
-    path tsv
-    tuple val(id), val(symbol)
-
-    output:
-    path "*.chip"       , emit: chip
-    path "versions.yml" , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def VERSION = '9.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    """
-    function find_column_number {
-        file=\$1
-        column=\$2
-
-        head -n 1 \$file | tr '\\t' '\\n' | grep -n "^\${column}\$" | awk -F':' '{print \$1}'
-    }
-
-    id_col=\$(find_column_number $tsv $id)
-    symbol_col=\$(find_column_number $tsv $symbol)
-    outfile=\$(echo $tsv | sed 's/\\(.*\\)\\..*/\\1/').chip
-
-    echo -e "Probe Set ID\\tGene Symbol\\tGene Title" > \${outfile}.tmp
-    tail -n +2 $tsv | awk -F'\\t' -v id=\$id_col -v symbol=\$symbol_col '{print \$id"\\t"\$symbol"\\tNA"}' >> \${outfile}.tmp
-    mv \${outfile}.tmp \${outfile}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch stub.chip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
-    END_VERSIONS
-    """
-
-}
diff --git a/modules/local/tabulartogseachip/meta.yml b/modules/local/tabulartogseachip/meta.yml
deleted file mode 100644
index aa9d7d93..00000000
--- a/modules/local/tabulartogseachip/meta.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-name: tabular_to_gsea_chip
-description: Convert tabular data into GSEA-compatible CHIP files.
-keywords:
-  - GSEA
-  - CHIP
-  - Bioinformatics
-tools:
-  - gawk:
-      description: |
-        GNU Awk (gawk) is a powerful programming language designed for text processing and typically used as a data extraction and reporting tool.
-        It is used here to manipulate tabular data and create the CHIP file format.
-      homepage: https://www.gnu.org/software/gawk/
-      documentation: https://www.gnu.org/software/gawk/manual/
-      licence: ["GPL-3.0-or-later"]
-input:
-  - tsv:
-      type: file
-      description: |
-        Tab-separated values (TSV) file containing data to be converted into a CHIP file.
-  - - id:
-        type: string
-        description: |
-          Feature ID attribute in the abundance table as well as in the GTF file (e.g. the gene_id field).
-    - symbol:
-        type: string
-        description: |
-          Feature name attribute in the abundance table as well as in the GTF file (e.g. the gene symbol field).
-output:
-  - chip:
-      type: file
-      description: Generated GSEA-compatible CHIP file.
-      pattern: "*.chip"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-authors:
-  - "@pinin4fjords" # Replace with actual author handles
-maintainers:
-  - "@nschcolnicov"
diff --git a/modules/local/tabulartogseachip/tests/main.nf.test b/modules/local/tabulartogseachip/tests/main.nf.test
deleted file mode 100644
index e6c5321b..00000000
--- a/modules/local/tabulartogseachip/tests/main.nf.test
+++ /dev/null
@@ -1,49 +0,0 @@
-nextflow_process {
-
-    name "Test Process TABULAR_TO_GSEA_CHIP"
-    script "../main.nf"
-    process "TABULAR_TO_GSEA_CHIP"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "tabular_to_gsea_chip"
-
-    test("test_tabular_to_gsea_chip") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.tsv")
-                input[1] = ["gene_id", "gene_name"]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() },
-            )
-        }
-    }
-
-    test("test_tabular_to_gsea_chip - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/modules_testdata/Mus_musculus.anno.feature_metadata.tsv")
-                input[1] = ["gene_id", "gene_name"]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() },
-            )
-        }
-    }
-}
diff --git a/modules/local/tabulartogseachip/tests/main.nf.test.snap b/modules/local/tabulartogseachip/tests/main.nf.test.snap
deleted file mode 100644
index 29d017ed..00000000
--- a/modules/local/tabulartogseachip/tests/main.nf.test.snap
+++ /dev/null
@@ -1,48 +0,0 @@
-{
-    "test_tabular_to_gsea_chip - stub": {
-        "content": [
-            {
-                "0": [
-                    "stub.chip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "1": [
-                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
-                ],
-                "chip": [
-                    "stub.chip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "versions": [
-                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-06T21:03:06.781994447"
-    },
-    "test_tabular_to_gsea_chip": {
-        "content": [
-            {
-                "0": [
-                    "Mus_musculus.anno.feature_metadata.chip:md5,5abf60bb982bb2ff5b8b3e37f14a21e4"
-                ],
-                "1": [
-                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
-                ],
-                "chip": [
-                    "Mus_musculus.anno.feature_metadata.chip:md5,5abf60bb982bb2ff5b8b3e37f14a21e4"
-                ],
-                "versions": [
-                    "versions.yml:md5,a422b1a01e86be433a25d1776d497f5a"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-06T21:02:58.608468636"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/tabulartogseachip/environment.yml b/modules/nf-core/custom/tabulartogseachip/environment.yml
similarity index 63%
rename from modules/local/tabulartogseachip/environment.yml
rename to modules/nf-core/custom/tabulartogseachip/environment.yml
index a6e8e310..cc49deff 100644
--- a/modules/local/tabulartogseachip/environment.yml
+++ b/modules/nf-core/custom/tabulartogseachip/environment.yml
@@ -1,6 +1,5 @@
 channels:
   - conda-forge
   - bioconda
-
 dependencies:
-  - conda-forge::gawk=5.1.0
+  - "conda-forge::gawk=5.1.0"
diff --git a/modules/nf-core/custom/tabulartogseachip/main.nf b/modules/nf-core/custom/tabulartogseachip/main.nf
new file mode 100644
index 00000000..c0622cda
--- /dev/null
+++ b/modules/nf-core/custom/tabulartogseachip/main.nf
@@ -0,0 +1,56 @@
+process CUSTOM_TABULARTOGSEACHIP {
+
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
+        'biocontainers/gawk:5.1.0' }"
+
+    input:
+    tuple val(meta), path(tabular)
+    tuple val(id)  , val(symbol)
+
+    output:
+    tuple val(meta), path("*.chip"), emit: chip
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    function find_column_number {
+        file=\$1
+        column=\$2
+
+        head -n 1 \$file | tr '\\t' '\\n' | grep -n "^\${column}\$" | awk -F':' '{print \$1}'
+    }
+
+    id_col=\$(find_column_number $tabular $id)
+    symbol_col=\$(find_column_number $tabular $symbol)
+    outfile=${prefix}.chip
+
+    echo -e "Probe Set ID\\tGene Symbol\\tGene Title" > \${outfile}.tmp
+    tail -n +2 $tabular | awk -F'\\t' -v id=\$id_col -v symbol=\$symbol_col '{print \$id"\\t"\$symbol"\\tNA"}' >> \${outfile}.tmp
+    mv \${outfile}.tmp \${outfile}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    outfile=${prefix}.chip
+    touch \$outfile
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/tabulartogseachip/meta.yml b/modules/nf-core/custom/tabulartogseachip/meta.yml
new file mode 100644
index 00000000..5759874c
--- /dev/null
+++ b/modules/nf-core/custom/tabulartogseachip/meta.yml
@@ -0,0 +1,53 @@
+name: "custom_tabulartogseachip"
+description: Make a GSEA class file (.chip) from tabular inputs
+keywords:
+  - gsea
+  - chip
+  - convert
+  - tabular
+tools:
+  - custom:
+      description: "Make a GSEA annotation file (.chip) from tabular inputs"
+      tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseachip/main.nf"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing data information.
+          This can be used at the workflow level to pass optional parameters to the module.
+          [id: 'test', ...]
+    - tabular:
+        type: file
+        description: |
+          Tabular (NOTE that for the moment it only works for TSV file) containing a column with the
+          features ids, and another column with the features symbols.
+        pattern: "*.{tsv}"
+  - - id:
+        type: string
+        description: The name of the column containing feature ids
+    - symbol:
+        type: string
+        description: The name of the column containing feature symbols
+output:
+  - chip:
+      - meta:
+          type: map
+          description: Groovy Map containing metadata e.g. [ id:'test', ... ]
+      - "*.chip":
+          type: file
+          description: |
+            A categorical class format file (.chip) as defined by the Broad
+            documentation at
+            https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
+          pattern: "*.chip"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@pinin4fjords"
+  - "@suzannejin"
+maintainers:
+  - "@pinin4fjords"
diff --git a/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test b/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test
new file mode 100644
index 00000000..6c2025a1
--- /dev/null
+++ b/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test
@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_TABULARTOGSEACHIP"
+    script "../main.nf"
+    process "CUSTOM_TABULARTOGSEACHIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom"
+    tag "custom/tabulartogseachip"
+
+    test("test tsv to chip") {
+
+        when {
+            process {
+                """
+                input[0] = Channel
+                    .fromPath(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                    .map { it -> [
+                        [id:it.baseName], it
+                    ]}
+                input[1] = Channel.of(['gene_id', 'gene_name'])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.chip,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("test tsv to chip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel
+                    .fromPath(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                    .map { it -> [
+                        [id:it.baseName], it
+                    ]}
+                input[1] = Channel.of(['gene_id', 'gene_name'])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.chip,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test.snap b/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test.snap
new file mode 100644
index 00000000..bb66d232
--- /dev/null
+++ b/modules/nf-core/custom/tabulartogseachip/tests/main.nf.test.snap
@@ -0,0 +1,42 @@
+{
+    "test tsv to chip": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "SRP254919.salmon.merged.gene_counts.top1000cov"
+                    },
+                    "SRP254919.salmon.merged.gene_counts.top1000cov.chip:md5,2ab8a685c675ce2fb97142526766044a"
+                ]
+            ],
+            [
+                "versions.yml:md5,61dab2d2b9aa1333c4c3bfd7bd893ce5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-16T18:05:22.341224384"
+    },
+    "test tsv to chip - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "SRP254919.salmon.merged.gene_counts.top1000cov"
+                    },
+                    "SRP254919.salmon.merged.gene_counts.top1000cov.chip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,61dab2d2b9aa1333c4c3bfd7bd893ce5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-17T13:14:53.792845507"
+    }
+}
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
index 37f61c5e..bbd6b2de 100644
--- a/tests/test.nf.test.snap
+++ b/tests/test.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             21,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "DESEQ2_DIFFERENTIAL": {
                     "r-base": "4.1.3",
                     "bioconductor-deseq2": "1.34.0"
@@ -23,9 +26,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -186,12 +186,15 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T11:56:20.743162854"
+        "timestamp": "2024-12-20T16:13:56.445211657"
     },
     "Test profile with yaml contrasts": {
         "content": [
             21,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "DESEQ2_DIFFERENTIAL": {
                     "r-base": "4.1.3",
                     "bioconductor-deseq2": "1.34.0"
@@ -212,9 +215,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -375,6 +375,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-20T13:41:10.4647836"
+        "timestamp": "2024-12-20T16:16:49.167979669"
     }
 }
\ No newline at end of file
diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap
index 2252b03a..4c0d12c1 100644
--- a/tests/test_affy.nf.test.snap
+++ b/tests/test_affy.nf.test.snap
@@ -7,6 +7,9 @@
                     "r-base": "4.3.1",
                     "bioconductor-affy": "1.78.0"
                 },
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "GSEA_GSEA": {
                     "gsea": "4.3.2"
                 },
@@ -21,9 +24,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -236,6 +236,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T12:03:13.731672183"
+        "timestamp": "2024-12-20T15:43:35.560675645"
     }
 }
\ No newline at end of file
diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap
index acd27efc..3e2b9af7 100644
--- a/tests/test_rnaseq_limma.nf.test.snap
+++ b/tests/test_rnaseq_limma.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             20,
             {
+                "CUSTOM_TABULARTOGSEACHIP": {
+                    "gawk": "5.1.0"
+                },
                 "GSEA_GSEA": {
                     "gsea": "4.3.2"
                 },
@@ -23,9 +26,6 @@
                 "PLOT_EXPLORATORY": {
                     "r-shinyngs": "2.0.0"
                 },
-                "TABULAR_TO_GSEA_CHIP": {
-                    "bash": "5.2.21 3"
-                },
                 "VALIDATOR": {
                     "r-base": "4.3.3",
                     "r-shinyngs": "2.0.0"
@@ -177,6 +177,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T12:10:44.503110769"
+        "timestamp": "2024-12-20T16:29:49.698674022"
     }
 }
\ No newline at end of file
diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
index 5a4faeb0..5f376041 100644
--- a/workflows/differentialabundance.nf
+++ b/workflows/differentialabundance.nf
@@ -98,7 +98,7 @@ citations_file = file(params.citations_file, checkIfExists: true)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { TABULAR_TO_GSEA_CHIP           } from '../modules/local/tabulartogseachip'
+include { CUSTOM_TABULARTOGSEACHIP       } from '../modules/nf-core/custom/tabulartogseachip/main'
 include { CUSTOM_FILTERDIFFERENTIALTABLE } from '../modules/nf-core/custom/filterdifferentialtable/main'
 
 /*
@@ -464,8 +464,8 @@ workflow DIFFERENTIALABUNDANCE {
 
         CUSTOM_TABULARTOGSEACLS(ch_contrasts_and_samples)
 
-        TABULAR_TO_GSEA_CHIP(
-            VALIDATOR.out.feature_meta.map{ it[1] },
+        CUSTOM_TABULARTOGSEACHIP(
+            VALIDATOR.out.feature_meta,
             [params.features_id_col, params.features_name_col]
         )
 
@@ -482,7 +482,7 @@ workflow DIFFERENTIALABUNDANCE {
         GSEA_GSEA(
             ch_gsea_inputs,
             ch_gsea_inputs.map{ tuple(it[0].reference, it[0].target) }, // *
-            TABULAR_TO_GSEA_CHIP.out.chip.first()
+            CUSTOM_TABULARTOGSEACHIP.out.chip.first().map{ it[1] }
         )
 
         // * Note: GSEA module currently uses a value channel for the mandatory
@@ -495,7 +495,7 @@ workflow DIFFERENTIALABUNDANCE {
 
         // Record GSEA versions
         ch_versions = ch_versions
-            .mix(TABULAR_TO_GSEA_CHIP.out.versions)
+            .mix(CUSTOM_TABULARTOGSEACHIP.out.versions)
             .mix(GSEA_GSEA.out.versions)
     }