From 62e1dae4c289a790ec31916da81d418cbadd3a3e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Wed, 29 Apr 2026 20:18:16 +0000
Subject: [PATCH 1/9] first draft of fgumi/extract

---
 modules/nf-core/fgumi/extract/environment.yml |  7 ++
 modules/nf-core/fgumi/extract/main.nf         | 40 +++++++++
 modules/nf-core/fgumi/extract/meta.yml        | 63 ++++++++++++++
 .../nf-core/fgumi/extract/tests/main.nf.test  | 61 ++++++++++++++
 .../fgumi/extract/tests/main.nf.test.snap     | 84 +++++++++++++++++++
 5 files changed, 255 insertions(+)
 create mode 100644 modules/nf-core/fgumi/extract/environment.yml
 create mode 100644 modules/nf-core/fgumi/extract/main.nf
 create mode 100644 modules/nf-core/fgumi/extract/meta.yml
 create mode 100644 modules/nf-core/fgumi/extract/tests/main.nf.test
 create mode 100644 modules/nf-core/fgumi/extract/tests/main.nf.test.snap

diff --git a/modules/nf-core/fgumi/extract/environment.yml b/modules/nf-core/fgumi/extract/environment.yml
new file mode 100644
index 000000000000..7960b0e5a1cf
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fgumi=0.2.0"
diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
new file mode 100644
index 000000000000..036ef5b845bf
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -0,0 +1,40 @@
+process FGUMI_EXTRACT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a5/a510706f3481fae12ff6100d6e4ad298b8bf464a2d93a6afe35e9cf26542d080/data'
+        : 'community.wave.seqera.io/library/fgumi:0.2.0--fe028e7a64e5da27'}"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val("${task.process}"), val('fgumi'), eval('fgumi --version | sed "s/^fgumi //"'), topic: versions, emit: versions_fgumi
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+    def sample = args.contains('--sample') ? '' : "--sample ${meta.id}"
+    def library = args.contains('--library') ? '' : "--library ${meta.id}"
+
+    """
+    fgumi extract \\
+        --inputs ${reads.join(' ')} \\
+        --output ${prefix}.bam \\
+        ${sample} \\
+        ${library} \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    touch ${prefix}.bam
+    """
+}
diff --git a/modules/nf-core/fgumi/extract/meta.yml b/modules/nf-core/fgumi/extract/meta.yml
new file mode 100644
index 000000000000..b11fbcfbd1c1
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/meta.yml
@@ -0,0 +1,63 @@
+name: fgumi_extract
+description: Extract unique molecular indices (UMIs) from FASTQ files and write an unaligned BAM file.
+keywords:
+  - umi
+  - extract
+  - fastq
+  - bam
+tools:
+  - fgumi:
+      description: High-performance tools for working with UMI-tagged sequencing data.
+      homepage: https://github.com/fulcrumgenomics/fgumi
+      documentation: https://docs.rs/fgumi
+      tool_dev_url: https://github.com/fulcrumgenomics/fgumi
+      licence: ["MIT"]
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: Input FASTQ files used for UMI extraction.
+        pattern: "*.fastq.gz"
+        ontologies: []
+output:
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Unaligned BAM with extracted UMIs in SAM tags.
+          pattern: "*.bam"
+          ontologies: []
+  versions_fgumi:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fgumi:
+          type: string
+          description: The tool name
+      - 'fgumi --version | sed "s/^fgumi //"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fgumi:
+          type: string
+          description: The tool name
+      - 'fgumi --version | sed "s/^fgumi //"':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@atrigila"
+maintainers:
+  - "@atrigila"
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test b/modules/nf-core/fgumi/extract/tests/main.nf.test
new file mode 100644
index 000000000000..1b0bdc26dd52
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process FGUMI_EXTRACT"
+    script "../main.nf"
+    process "FGUMI_EXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fgumi"
+    tag "fgumi/extract"
+
+    test("homo_sapiens - [fastq1, fastq2]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [fastq1, fastq2] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
new file mode 100644
index 000000000000..51efe1a38baa
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
@@ -0,0 +1,84 @@
+{
+    "homo_sapiens - [fastq1, fastq2]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,0b06fac2943d2128fbb391f7da0948e3"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FGUMI_EXTRACT",
+                        "fgumi",
+                        "0.2.0"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,0b06fac2943d2128fbb391f7da0948e3"
+                    ]
+                ],
+                "versions_fgumi": [
+                    [
+                        "FGUMI_EXTRACT",
+                        "fgumi",
+                        "0.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T20:16:44.87275989",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - [fastq1, fastq2] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FGUMI_EXTRACT",
+                        "fgumi",
+                        "0.2.0"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_fgumi": [
+                    [
+                        "FGUMI_EXTRACT",
+                        "fgumi",
+                        "0.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T19:49:25.098129043",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file

From 58c621fe3c5dcdaeeee82558ede9b8a38c82e631 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Mon, 4 May 2026 22:22:44 +0200
Subject: [PATCH 2/9] update fgumi

---
 modules/nf-core/fgumi/extract/main.nf         | 13 +++---
 .../nf-core/fgumi/extract/tests/main.nf.test  | 44 ++++++++++++++++++-
 .../fgumi/extract/tests/main.nf.test.snap     | 34 +-------------
 .../fgumi/extract/tests/nextflow.config       |  6 +++
 4 files changed, 56 insertions(+), 41 deletions(-)
 create mode 100644 modules/nf-core/fgumi/extract/tests/nextflow.config

diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
index 036ef5b845bf..75369c834394 100644
--- a/modules/nf-core/fgumi/extract/main.nf
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -1,6 +1,6 @@
 process FGUMI_EXTRACT {
     tag "${meta.id}"
-    label 'process_low'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
@@ -19,21 +19,20 @@ process FGUMI_EXTRACT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: meta.id
-    def sample = args.contains('--sample') ? '' : "--sample ${meta.id}"
-    def library = args.contains('--library') ? '' : "--library ${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (!args.contains('--sample') || !args.contains('--library')) {
+        error("fgumi extract requires both --sample and --library to be supplied via task.ext.args")
+    }
 
     """
     fgumi extract \\
         --inputs ${reads.join(' ')} \\
         --output ${prefix}.bam \\
-        ${sample} \\
-        ${library} \\
         ${args}
     """
 
     stub:
-    def prefix = task.ext.prefix ?: meta.id
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
     """
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test b/modules/nf-core/fgumi/extract/tests/main.nf.test
index 1b0bdc26dd52..373d5ee85291 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test
@@ -9,9 +9,15 @@ nextflow_process {
     tag "fgumi"
     tag "fgumi/extract"
 
+    config "./nextflow.config"
+
     test("homo_sapiens - [fastq1, fastq2]") {
 
         when {
+            params {
+                module_args = '--library test'
+                prefix = ''
+            }
             process {
                 """
                 input[0] = [
@@ -27,17 +33,50 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert snapshot(process.out).match() }
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 
     }
 
+    test("homo_sapiens - [fastq1, fastq2] - missing library") {
+
+        when {
+            params {
+                module_args = '--read-structures +T +M'
+                prefix = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !process.success },
+                { assert process.errorReport.contains('fgumi extract requires both --sample and --library') }
+            )
+            }
+    }
+
     test("homo_sapiens - [fastq1, fastq2] - stub") {
 
         options "-stub"
 
         when {
+            params {
+                module_args = "--sample test --library test --read-structures +T +M"
+                prefix = ''
+            }
             process {
                 """
                 input[0] = [
@@ -53,7 +92,8 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert snapshot(process.out).match() }
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
index 51efe1a38baa..1bba8ef32d0f 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
@@ -2,21 +2,6 @@
     "homo_sapiens - [fastq1, fastq2]": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bam:md5,0b06fac2943d2128fbb391f7da0948e3"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FGUMI_EXTRACT",
-                        "fgumi",
-                        "0.2.0"
-                    ]
-                ],
                 "bam": [
                     [
                         {
@@ -34,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-29T20:16:44.87275989",
+        "timestamp": "2026-05-04T22:22:16.912892888",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -43,21 +28,6 @@
     "homo_sapiens - [fastq1, fastq2] - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FGUMI_EXTRACT",
-                        "fgumi",
-                        "0.2.0"
-                    ]
-                ],
                 "bam": [
                     [
                         {
@@ -75,7 +45,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-29T19:49:25.098129043",
+        "timestamp": "2026-05-04T22:10:38.368295554",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
diff --git a/modules/nf-core/fgumi/extract/tests/nextflow.config b/modules/nf-core/fgumi/extract/tests/nextflow.config
new file mode 100644
index 000000000000..2cc0d7b7268d
--- /dev/null
+++ b/modules/nf-core/fgumi/extract/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: FGUMI_EXTRACT {
+        ext.args   = { "--sample ${meta.id} ${params.module_args}" }
+        ext.prefix = params.prefix
+    }
+}
\ No newline at end of file

From 84e5bfcaa572b8c72c3a70c48d14870398d7b7a6 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Tue, 5 May 2026 17:50:05 +0200
Subject: [PATCH 3/9] add library

---
 modules/nf-core/fgumi/extract/tests/main.nf.test      | 2 +-
 modules/nf-core/fgumi/extract/tests/main.nf.test.snap | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test b/modules/nf-core/fgumi/extract/tests/main.nf.test
index 373d5ee85291..5a610bd0c6f0 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = '--library test'
+                module_args = '--library illumina'
                 prefix = ''
             }
             process {
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
index 1bba8ef32d0f..c8ea4ce2adad 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,0b06fac2943d2128fbb391f7da0948e3"
+                        "test.bam:md5,9c2476e5c354f57bed109e582b8953be"
                     ]
                 ],
                 "versions_fgumi": [
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-04T22:22:16.912892888",
+        "timestamp": "2026-05-05T17:49:43.490283983",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From 517df53b3eba99b7300e824c127a0dbd0acb7a23 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 12:40:59 +0000
Subject: [PATCH 4/9] add default prefix, fix linting

---
 modules/nf-core/fgumi/extract/main.nf                |  4 ++--
 .../nf-core/fgumi/extract/tests/main.nf.test.snap    | 12 ++++++------
 modules/nf-core/fgumi/extract/tests/nextflow.config  |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
index 75369c834394..a7b01a5b019d 100644
--- a/modules/nf-core/fgumi/extract/main.nf
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -19,7 +19,7 @@ process FGUMI_EXTRACT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}.fgumi_extract"
     if (!args.contains('--sample') || !args.contains('--library')) {
         error("fgumi extract requires both --sample and --library to be supplied via task.ext.args")
     }
@@ -32,7 +32,7 @@ process FGUMI_EXTRACT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}.fgumi_extract"
     """
     touch ${prefix}.bam
     """
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
index c8ea4ce2adad..a9cb8e883913 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,9c2476e5c354f57bed109e582b8953be"
+                        "test.fgumi_extract.bam:md5,8d7b8ec04bbfe4285cddced4c82aea7d"
                     ]
                 ],
                 "versions_fgumi": [
@@ -19,10 +19,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-05T17:49:43.490283983",
+        "timestamp": "2026-05-07T12:35:44.755887347",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.0"
         }
     },
     "homo_sapiens - [fastq1, fastq2] - stub": {
@@ -33,7 +33,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.fgumi_extract.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_fgumi": [
@@ -45,10 +45,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-04T22:10:38.368295554",
+        "timestamp": "2026-05-07T12:36:12.822185537",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fgumi/extract/tests/nextflow.config b/modules/nf-core/fgumi/extract/tests/nextflow.config
index 2cc0d7b7268d..de08c1b03ce7 100644
--- a/modules/nf-core/fgumi/extract/tests/nextflow.config
+++ b/modules/nf-core/fgumi/extract/tests/nextflow.config
@@ -3,4 +3,4 @@ process {
         ext.args   = { "--sample ${meta.id} ${params.module_args}" }
         ext.prefix = params.prefix
     }
-}
\ No newline at end of file
+}

From 045536e863ef58ba5300000e0f7cf01e54339f67 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 12:50:58 +0000
Subject: [PATCH 5/9] remove default prefix

---
 modules/nf-core/fgumi/extract/main.nf                 | 4 ++--
 modules/nf-core/fgumi/extract/tests/main.nf.test.snap | 8 ++++----
 modules/nf-core/fgumi/extract/tests/nextflow.config   | 1 -
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
index a7b01a5b019d..75369c834394 100644
--- a/modules/nf-core/fgumi/extract/main.nf
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -19,7 +19,7 @@ process FGUMI_EXTRACT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}.fgumi_extract"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     if (!args.contains('--sample') || !args.contains('--library')) {
         error("fgumi extract requires both --sample and --library to be supplied via task.ext.args")
     }
@@ -32,7 +32,7 @@ process FGUMI_EXTRACT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}.fgumi_extract"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
     """
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
index a9cb8e883913..8c054cafd78c 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fgumi_extract.bam:md5,8d7b8ec04bbfe4285cddced4c82aea7d"
+                        "test.bam:md5,9c2476e5c354f57bed109e582b8953be"
                     ]
                 ],
                 "versions_fgumi": [
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-07T12:35:44.755887347",
+        "timestamp": "2026-05-07T12:48:51.477812468",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -33,7 +33,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fgumi_extract.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_fgumi": [
@@ -45,7 +45,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-07T12:36:12.822185537",
+        "timestamp": "2026-05-07T12:49:21.767581495",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
diff --git a/modules/nf-core/fgumi/extract/tests/nextflow.config b/modules/nf-core/fgumi/extract/tests/nextflow.config
index de08c1b03ce7..3462c8fa06f7 100644
--- a/modules/nf-core/fgumi/extract/tests/nextflow.config
+++ b/modules/nf-core/fgumi/extract/tests/nextflow.config
@@ -1,6 +1,5 @@
 process {
     withName: FGUMI_EXTRACT {
         ext.args   = { "--sample ${meta.id} ${params.module_args}" }
-        ext.prefix = params.prefix
     }
 }

From 84535d093fc2ac52618eae94ad57821273b9d06c Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 13:03:30 +0000
Subject: [PATCH 6/9] remove unused prefix

---
 modules/nf-core/fgumi/extract/tests/main.nf.test | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test b/modules/nf-core/fgumi/extract/tests/main.nf.test
index 5a610bd0c6f0..2a511eaef5fa 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test
@@ -16,7 +16,6 @@ nextflow_process {
         when {
             params {
                 module_args = '--library illumina'
-                prefix = ''
             }
             process {
                 """
@@ -45,7 +44,6 @@ nextflow_process {
         when {
             params {
                 module_args = '--read-structures +T +M'
-                prefix = ''
             }
             process {
                 """
@@ -75,7 +73,6 @@ nextflow_process {
         when {
             params {
                 module_args = "--sample test --library test --read-structures +T +M"
-                prefix = ''
             }
             process {
                 """

From c960d2e5f0be1b3831eebb75b71dc8da7994d0cf Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 16:50:27 +0000
Subject: [PATCH 7/9] add sample and library as mandatory args

---
 modules/nf-core/fgumi/extract/main.nf               | 7 +++----
 modules/nf-core/fgumi/extract/meta.yml              | 6 ++++++
 modules/nf-core/fgumi/extract/tests/nextflow.config | 2 +-
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
index 75369c834394..214452691d70 100644
--- a/modules/nf-core/fgumi/extract/main.nf
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -8,7 +8,7 @@ process FGUMI_EXTRACT {
         : 'community.wave.seqera.io/library/fgumi:0.2.0--fe028e7a64e5da27'}"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads), val(sample), val(library)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -20,14 +20,13 @@ process FGUMI_EXTRACT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (!args.contains('--sample') || !args.contains('--library')) {
-        error("fgumi extract requires both --sample and --library to be supplied via task.ext.args")
-    }
 
     """
     fgumi extract \\
         --inputs ${reads.join(' ')} \\
         --output ${prefix}.bam \\
+        --sample "${sample}" \\
+        --library "${library}" \\
         ${args}
     """
 
diff --git a/modules/nf-core/fgumi/extract/meta.yml b/modules/nf-core/fgumi/extract/meta.yml
index b11fbcfbd1c1..a7d3288986b6 100644
--- a/modules/nf-core/fgumi/extract/meta.yml
+++ b/modules/nf-core/fgumi/extract/meta.yml
@@ -23,6 +23,12 @@ input:
         description: Input FASTQ files used for UMI extraction.
         pattern: "*.fastq.gz"
         ontologies: []
+    - sample:
+        type: string
+        description: Sample name to store in the output BAM read group.
+    - library:
+        type: string
+        description: Library name to store in the output BAM read group.
 output:
   bam:
     - - meta:
diff --git a/modules/nf-core/fgumi/extract/tests/nextflow.config b/modules/nf-core/fgumi/extract/tests/nextflow.config
index 3462c8fa06f7..54ef88450854 100644
--- a/modules/nf-core/fgumi/extract/tests/nextflow.config
+++ b/modules/nf-core/fgumi/extract/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: FGUMI_EXTRACT {
-        ext.args   = { "--sample ${meta.id} ${params.module_args}" }
+        ext.args   = { "${params.module_args}" }
     }
 }

From 6351f2c575cade557ae972f2c07473b7ac47936e Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 18:45:46 +0000
Subject: [PATCH 8/9] update tests

---
 modules/nf-core/fgumi/extract/main.nf         |  8 ++--
 .../nf-core/fgumi/extract/tests/main.nf.test  | 37 +++----------------
 2 files changed, 10 insertions(+), 35 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/main.nf b/modules/nf-core/fgumi/extract/main.nf
index 214452691d70..fb17d5adf0d5 100644
--- a/modules/nf-core/fgumi/extract/main.nf
+++ b/modules/nf-core/fgumi/extract/main.nf
@@ -8,7 +8,7 @@ process FGUMI_EXTRACT {
         : 'community.wave.seqera.io/library/fgumi:0.2.0--fe028e7a64e5da27'}"
 
     input:
-    tuple val(meta), path(reads), val(sample), val(library)
+    tuple val(meta), path(reads), val(library)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -25,9 +25,9 @@ process FGUMI_EXTRACT {
     fgumi extract \\
         --inputs ${reads.join(' ')} \\
         --output ${prefix}.bam \\
-        --sample "${sample}" \\
-        --library "${library}" \\
-        ${args}
+        ${args} \\
+        --sample ${prefix} \\
+        --library "${library}"
     """
 
     stub:
diff --git a/modules/nf-core/fgumi/extract/tests/main.nf.test b/modules/nf-core/fgumi/extract/tests/main.nf.test
index 2a511eaef5fa..44ce2572e72d 100644
--- a/modules/nf-core/fgumi/extract/tests/main.nf.test
+++ b/modules/nf-core/fgumi/extract/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = '--library illumina'
+                module_args = ''
             }
             process {
                 """
@@ -24,7 +24,8 @@ nextflow_process {
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
-                    ]
+                    ],
+                    'illumina',
                 ]
                 """
             }
@@ -39,40 +40,13 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [fastq1, fastq2] - missing library") {
-
-        when {
-            params {
-                module_args = '--read-structures +T +M'
-            }
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
-                    ]
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert !process.success },
-                { assert process.errorReport.contains('fgumi extract requires both --sample and --library') }
-            )
-            }
-    }
-
     test("homo_sapiens - [fastq1, fastq2] - stub") {
 
         options "-stub"
 
         when {
             params {
-                module_args = "--sample test --library test --read-structures +T +M"
+                module_args = "--read-structures +T +M"
             }
             process {
                 """
@@ -81,7 +55,8 @@ nextflow_process {
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz', checkIfExists: true),
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz', checkIfExists: true)
-                    ]
+                    ],
+                    'test',
                 ]
                 """
             }

From cfef819fbeb25a313d04c24f824c8f4c5fd4e9e3 Mon Sep 17 00:00:00 2001
From: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Date: Thu, 7 May 2026 18:51:40 +0000
Subject: [PATCH 9/9] fix linting

---
 modules/nf-core/fgumi/extract/meta.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/fgumi/extract/meta.yml b/modules/nf-core/fgumi/extract/meta.yml
index a7d3288986b6..7d62b590c47e 100644
--- a/modules/nf-core/fgumi/extract/meta.yml
+++ b/modules/nf-core/fgumi/extract/meta.yml
@@ -1,5 +1,6 @@
 name: fgumi_extract
-description: Extract unique molecular indices (UMIs) from FASTQ files and write an unaligned BAM file.
+description: Extract unique molecular indices (UMIs) from FASTQ files and write
+  an unaligned BAM file.
 keywords:
   - umi
   - extract
@@ -7,11 +8,14 @@ keywords:
   - bam
 tools:
   - fgumi:
-      description: High-performance tools for working with UMI-tagged sequencing data.
+      description: High-performance tools for working with UMI-tagged sequencing
+        data.
       homepage: https://github.com/fulcrumgenomics/fgumi
       documentation: https://docs.rs/fgumi
       tool_dev_url: https://github.com/fulcrumgenomics/fgumi
-      licence: ["MIT"]
+      licence:
+        - "MIT"
+      identifier: ""
 input:
   - - meta:
         type: map
@@ -22,10 +26,8 @@ input:
         type: file
         description: Input FASTQ files used for UMI extraction.
         pattern: "*.fastq.gz"
-        ontologies: []
-    - sample:
-        type: string
-        description: Sample name to store in the output BAM read group.
+        ontologies:
+          - edam: http://edamontology.org/format_3989
     - library:
         type: string
         description: Library name to store in the output BAM read group.
@@ -51,7 +53,6 @@ output:
       - 'fgumi --version | sed "s/^fgumi //"':
           type: eval
           description: The expression to obtain the version of the tool
-
 topics:
   versions:
     - - ${task.process}: