From 2ad3c794d5a5d44a8a3003d0abf1462914b87d00 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Tue, 25 Nov 2025 17:28:33 +0000
Subject: [PATCH 1/8] Add module pbmarkdup

---
 modules/nf-core/pbmarkdup/environment.yml     |   7 ++
 modules/nf-core/pbmarkdup/main.nf             |  50 +++++++++
 modules/nf-core/pbmarkdup/meta.yml            |  58 ++++++++++
 modules/nf-core/pbmarkdup/tests/main.nf.test  |  91 ++++++++++++++++
 .../nf-core/pbmarkdup/tests/main.nf.test.snap | 101 ++++++++++++++++++
 .../nf-core/pbmarkdup/tests/nextflow.config   |   5 +
 6 files changed, 312 insertions(+)
 create mode 100644 modules/nf-core/pbmarkdup/environment.yml
 create mode 100644 modules/nf-core/pbmarkdup/main.nf
 create mode 100644 modules/nf-core/pbmarkdup/meta.yml
 create mode 100644 modules/nf-core/pbmarkdup/tests/main.nf.test
 create mode 100644 modules/nf-core/pbmarkdup/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/pbmarkdup/tests/nextflow.config

diff --git a/modules/nf-core/pbmarkdup/environment.yml b/modules/nf-core/pbmarkdup/environment.yml
new file mode 100644
index 000000000000..4484c5763827
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/sanger-tol/nf-core-modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::pbmarkdup==1.2.0
\ No newline at end of file
diff --git a/modules/nf-core/pbmarkdup/main.nf b/modules/nf-core/pbmarkdup/main.nf
new file mode 100644
index 000000000000..e6640bd1e900
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/main.nf
@@ -0,0 +1,50 @@
+process PBMARKDUP {
+    tag "$meta.id"
+    label "process_high"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pbmarkdup:1.2.0--h9ee0642_0' :
+        'biocontainers/pbmarkdup:1.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*.{bam,f*a,/.*f.*\\.gz/}") , emit: markduped
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args  = task.ext.args  ?: ''
+
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = input.getExtension()
+
+    """
+    pbmarkdup \\
+        -j ${task.cpus} \\
+        $input \\
+        ${prefix}.${suffix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbmarkdup: \$(echo \$(pbmarkdup --version 2>&1) | awk 'BEFORE{FS=" "}{print \$2}')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = input.getExtension()
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbmarkdup: \$(echo \$(pbmarkdup --version 2>&1) | awk 'BEFORE{FS=" "}{print \$2}')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/pbmarkdup/meta.yml b/modules/nf-core/pbmarkdup/meta.yml
new file mode 100644
index 000000000000..3dcde7b27b99
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/meta.yml
@@ -0,0 +1,58 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbmarkdup"
+description: |
+  Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes 
+  duplicates.
+keywords:
+  - markdup
+  - bam
+  - fastq
+  - fasta
+tools:
+  - pbmarkdup:
+      description: |
+        pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters 
+        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output 
+        (duplicate bit 0x400), optionally removing duplicates. 
+      homepage: https://github.com/PacificBiosciences/pbmarkdup
+      documentation: https://github.com/PacificBiosciences/pbmarkdup
+      licence: ["BSD-3-Clause"]
+      identifier: biotools:pbmarkdup
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - input:
+        type: file
+        description: |
+          Sequencing reads in BAM, FASTQ, or FASTA format.
+        pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
+        ontologies:
+          - edam: http://edamontology.org/format_2546 # FASTA-like
+output:
+  markduped:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.${suffix}":
+          type: file
+          description: |
+            Markduplicated sequencing reads in the same format as the input file.
+          pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
+          ontologies:
+            - edam: http://edamontology.org/format_3003
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@sainsachiko"
+maintainers:
+  - "@sainsachiko"
\ No newline at end of file
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
new file mode 100644
index 000000000000..fe9a17389be6
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -0,0 +1,91 @@
+
+nextflow_process {
+
+    name "Test Process PBMARKDUP"
+    script "../main.nf"
+    process "PBMARKDUP"
+
+    tag "modules"
+    tag "modules_sangertol"
+    tag "pbmarkdup"
+
+    config './nextflow.config'
+
+    test("deilephila porcellus - fasta") {
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("acropora cervicornis - bam") {
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ], // meta map
+                        file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.resubset.bam', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("deilephila porcellus - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test.snap b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
new file mode 100644
index 000000000000..c719f3f5abea
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "acropora cervicornis - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,63490fcddb44783b761fab8e54123d73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "markduped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,63490fcddb44783b761fab8e54123d73"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-25T13:57:29.646511931"
+    },
+    "deilephila porcellus - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "markduped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-25T13:43:50.757401556"
+    },
+    "deilephila porcellus - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,087cee5291f8d728a62b91765b64af35"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "markduped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,087cee5291f8d728a62b91765b64af35"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-25T13:43:28.330988318"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pbmarkdup/tests/nextflow.config b/modules/nf-core/pbmarkdup/tests/nextflow.config
new file mode 100644
index 000000000000..033dac0673a2
--- /dev/null
+++ b/modules/nf-core/pbmarkdup/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PBMARKDUP {
+        ext.args = { "--clobber" }
+    }
+}

From 9239d22fd83eb96560caef2009420b7f44b3bf6e Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 26 Nov 2025 02:01:34 +0700
Subject: [PATCH 2/8] Fix linting

---
 modules/nf-core/pbmarkdup/environment.yml    |  2 +-
 modules/nf-core/pbmarkdup/main.nf            | 12 ++++++------
 modules/nf-core/pbmarkdup/meta.yml           | 18 +++++++++++-------
 modules/nf-core/pbmarkdup/tests/main.nf.test |  2 +-
 4 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/pbmarkdup/environment.yml b/modules/nf-core/pbmarkdup/environment.yml
index 4484c5763827..7e5a3099a716 100644
--- a/modules/nf-core/pbmarkdup/environment.yml
+++ b/modules/nf-core/pbmarkdup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pbmarkdup==1.2.0
\ No newline at end of file
+  - bioconda::pbmarkdup=1.2.0
diff --git a/modules/nf-core/pbmarkdup/main.nf b/modules/nf-core/pbmarkdup/main.nf
index e6640bd1e900..c9f351952a98 100644
--- a/modules/nf-core/pbmarkdup/main.nf
+++ b/modules/nf-core/pbmarkdup/main.nf
@@ -11,8 +11,8 @@ process PBMARKDUP {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.{bam,f*a,/.*f.*\\.gz/}") , emit: markduped
-    path "versions.yml"                               , emit: versions
+    tuple val(meta), path("${prefix}.${suffix}"), emit: markduped
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,8 +20,8 @@ process PBMARKDUP {
     script:
     def args  = task.ext.args  ?: ''
 
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = input.getExtension()
+    prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = input.getExtension()
 
     """
     pbmarkdup \\
@@ -37,8 +37,8 @@ process PBMARKDUP {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = input.getExtension()
+    prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = input.getExtension()
     """
     touch ${prefix}.${suffix}
 
diff --git a/modules/nf-core/pbmarkdup/meta.yml b/modules/nf-core/pbmarkdup/meta.yml
index 3dcde7b27b99..7762b0d78b14 100644
--- a/modules/nf-core/pbmarkdup/meta.yml
+++ b/modules/nf-core/pbmarkdup/meta.yml
@@ -1,7 +1,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "pbmarkdup"
 description: |
-  Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes 
+  Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes
   duplicates.
 keywords:
   - markdup
@@ -11,9 +11,9 @@ keywords:
 tools:
   - pbmarkdup:
       description: |
-        pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters 
-        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output 
-        (duplicate bit 0x400), optionally removing duplicates. 
+        pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters
+        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output
+        (duplicate bit 0x400), optionally removing duplicates.
       homepage: https://github.com/PacificBiosciences/pbmarkdup
       documentation: https://github.com/PacificBiosciences/pbmarkdup
       licence: ["BSD-3-Clause"]
@@ -31,6 +31,8 @@ input:
         pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
         ontologies:
           - edam: http://edamontology.org/format_2546 # FASTA-like
+          - edam: "http://edamontology.org/format_1930" # FASTQ
+          - edam: "http://edamontology.org/format_2572" # BAM
 output:
   markduped:
     - - meta:
@@ -38,13 +40,15 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1' ]`
-      - "*.${suffix}":
+      - ${prefix}.${suffix}:
           type: file
           description: |
             Markduplicated sequencing reads in the same format as the input file.
           pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
           ontologies:
-            - edam: http://edamontology.org/format_3003
+            - edam: http://edamontology.org/format_2546 # FASTA-like
+            - edam: "http://edamontology.org/format_1930" # FASTQ
+            - edam: "http://edamontology.org/format_2572" # BAM
   versions:
     - versions.yml:
         type: file
@@ -55,4 +59,4 @@ output:
 authors:
   - "@sainsachiko"
 maintainers:
-  - "@sainsachiko"
\ No newline at end of file
+  - "@sainsachiko"
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
index fe9a17389be6..cdbd594d4ca3 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     process "PBMARKDUP"
 
     tag "modules"
-    tag "modules_sangertol"
+    tag "modules_nfcore"
     tag "pbmarkdup"
 
     config './nextflow.config'

From 2a75dc8a8738e50eb0f2c09d58d59ab681952611 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Wed, 26 Nov 2025 16:25:43 +0700
Subject: [PATCH 3/8] Update path to test data

---
 modules/nf-core/pbmarkdup/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
index cdbd594d4ca3..6ad9a1fa3311 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -45,7 +45,7 @@ nextflow_process {
                 input[0] = Channel.of(
                     [
                         [ id:'test' ], // meta map
-                        file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.resubset.bam', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.resubset.bam', checkIfExists: true)
                     ]
                 )
                 """

From 4d913d69316afd6a6c379c0bccc723a68ed16d30 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 27 Nov 2025 22:09:51 +0700
Subject: [PATCH 4/8] Update with code review (--dup-file, log, check file name
 collisions)

---
 modules/nf-core/pbmarkdup/main.nf             |  37 ++++-
 modules/nf-core/pbmarkdup/tests/main.nf.test  |  46 ++++++-
 .../nf-core/pbmarkdup/tests/main.nf.test.snap | 129 ++++++++++++++++--
 .../nf-core/pbmarkdup/tests/nextflow.config   |   4 +-
 4 files changed, 196 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/pbmarkdup/main.nf b/modules/nf-core/pbmarkdup/main.nf
index c9f351952a98..287e887be5eb 100644
--- a/modules/nf-core/pbmarkdup/main.nf
+++ b/modules/nf-core/pbmarkdup/main.nf
@@ -12,23 +12,42 @@ process PBMARKDUP {
 
     output:
     tuple val(meta), path("${prefix}.${suffix}"), emit: markduped
+    tuple val(meta), path("${dupfile_name}")    , emit: dupfile   , optional: true
+    tuple val(meta), path("*.pbmarkdup.log")    , emit: logs      , optional: true
     path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args  = task.ext.args  ?: ''
+    def args     = task.ext.args  ?: ''
+    prefix       = task.ext.prefix ?: "${meta.id}"
+    suffix       = input[0].getExtension()             // To allow multiple input types
+    dupfile_name = args.contains('--dup-file') ? (args =~ /--dup-file\s+(\S+)/)[0][1] : ''
+    def log_args = args.contains('--log-level') ? " > ${prefix}.pbmarkdup.log" : ''
+    def file_list = input.collect { it.getName() }.join(' ')
 
-    prefix = task.ext.prefix ?: "${meta.id}"
-    suffix = input.getExtension()
+    // Check file name collisions between input, output, and duplicate file
+    if (file_list.contains("${prefix}.${suffix}")) 
+        error """Output file `${prefix}.${suffix}` conflicts with an input file.
+        Please change the output `$prefix` or input file names."""
+    if (dupfile_name) {
+        if (file_list.contains(dupfile_name)) 
+            error """Duplicate file `$dupfile_name` conflicts with an input file.
+            Please change the duplicate file name `$dupfile_name` or input file names."""
+
+        if (dupfile_name == "${prefix}.${suffix}") 
+            error """Duplicate file `$dupfile_name` cannot be the same as the output file name.
+            Please change the duplicate file name `$dupfile_name` or output prefix `$prefix`."""
+    }
 
     """
     pbmarkdup \\
         -j ${task.cpus} \\
-        $input \\
+        ${file_list} \\
         ${prefix}.${suffix} \\
-        $args
+        $args \\
+        ${log_args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,8 +56,12 @@ process PBMARKDUP {
     """
 
     stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
-    suffix = input.getExtension()
+    def args      = task.ext.args  ?: ''
+    prefix        = task.ext.prefix ?: "${meta.id}"
+    suffix        = input[0].getExtension()             // To allow multiple input types
+    dupfile_name  = args.contains('--dup-file') ? (args =~ /--dup-file\s+(\S+)/)[0][1] : ''
+    def log_args  = args.contains('--log-level') ? " > ${prefix}.pbmarkdup.log" : ''
+    def file_list = input.collect { it.getName() }.join(' ')
     """
     touch ${prefix}.${suffix}
 
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
index 6ad9a1fa3311..34d19a058837 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -15,6 +15,10 @@ nextflow_process {
 
         when {
 
+            params {
+                pbmarkdup_args = "--clobber --dup-file output.dup.fasta"
+            }
+
             process {
                 """
                 input[0] = Channel.of(
@@ -36,16 +40,51 @@ nextflow_process {
 
     }
 
-    test("acropora cervicornis - bam") {
+    test("acropora cervicornis - bam - multiple tests with dupfile and log") {
+        when {
+
+            params {
+                pbmarkdup_args = "--clobber --dup-file ${prefix}.dup.bam --log-level INFO"
+            }
+
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ], // meta map
+                        [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
+                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true) 
+                        ]
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 
+    test("acropora cervicornis - bam - multiple tests remove duplicates") {
         when {
 
+            params {
+                pbmarkdup_args = "--clobber --rmdup"
+            }
+
             process {
                 """
                 input[0] = Channel.of(
                     [
                         [ id:'test' ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.resubset.bam', checkIfExists: true)
+                        [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
+                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true) 
+                        ]
                     ]
                 )
                 """
@@ -66,6 +105,9 @@ nextflow_process {
         options "-stub"
 
         when {
+            params {
+                pbmarkdup_args = ""
+            }
 
             process {
                 """
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test.snap b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
index c719f3f5abea..31ae76263b3a 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "acropora cervicornis - bam": {
+    "acropora cervicornis - bam - multiple tests remove duplicates": {
         "content": [
             {
                 "0": [
@@ -7,18 +7,95 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,63490fcddb44783b761fab8e54123d73"
+                        "test.bam:md5,86e22a794d904cc48cb3758a03883ba1"
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "dupfile": [
+                    
+                ],
+                "logs": [
+                    
+                ],
+                "markduped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,86e22a794d904cc48cb3758a03883ba1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-11-27T22:01:01.517309"
+    },
+    "acropora cervicornis - bam - multiple tests with dupfile and log": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,86e22a794d904cc48cb3758a03883ba1"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "null.dup.bam:md5,3b74225ad5f7e9e1cbafc45132ad82fb"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pbmarkdup.log:md5,99987a1331d01b59aa3b5ccd1c787906"
+                    ]
+                ],
+                "3": [
                     "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
                 ],
+                "dupfile": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "null.dup.bam:md5,3b74225ad5f7e9e1cbafc45132ad82fb"
+                    ]
+                ],
+                "logs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pbmarkdup.log:md5,99987a1331d01b59aa3b5ccd1c787906"
+                    ]
+                ],
                 "markduped": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,63490fcddb44783b761fab8e54123d73"
+                        "test.bam:md5,86e22a794d904cc48cb3758a03883ba1"
                     ]
                 ],
                 "versions": [
@@ -28,9 +105,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-25T13:57:29.646511931"
+        "timestamp": "2025-11-27T22:00:33.750177"
     },
     "deilephila porcellus - stub": {
         "content": [
@@ -44,7 +121,19 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
                     "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "dupfile": [
+                    
+                ],
+                "logs": [
+                    
                 ],
                 "markduped": [
                     [
@@ -61,9 +150,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-25T13:43:50.757401556"
+        "timestamp": "2025-11-27T22:01:14.242019"
     },
     "deilephila porcellus - fasta": {
         "content": [
@@ -77,7 +166,29 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "output.dup.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
                     "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
+                ],
+                "dupfile": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "output.dup.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "logs": [
+                    
                 ],
                 "markduped": [
                     [
@@ -94,8 +205,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-25T13:43:28.330988318"
+        "timestamp": "2025-11-27T22:00:02.071951"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pbmarkdup/tests/nextflow.config b/modules/nf-core/pbmarkdup/tests/nextflow.config
index 033dac0673a2..38bce1a3ac67 100644
--- a/modules/nf-core/pbmarkdup/tests/nextflow.config
+++ b/modules/nf-core/pbmarkdup/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: PBMARKDUP {
-        ext.args = { "--clobber" }
+        ext.args = { "${params.pbmarkdup_args}" }
     }
-}
+}
\ No newline at end of file

From 1271655db67e4cffc9d87002a2e6f696c87b0c9c Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 27 Nov 2025 22:50:58 +0700
Subject: [PATCH 5/8] Fix linting

---
 modules/nf-core/pbmarkdup/main.nf             |  8 ++---
 modules/nf-core/pbmarkdup/meta.yml            | 27 +++++++++++++++++
 modules/nf-core/pbmarkdup/tests/main.nf.test  |  6 ++--
 .../nf-core/pbmarkdup/tests/main.nf.test.snap | 30 +++++++------------
 .../nf-core/pbmarkdup/tests/nextflow.config   |  2 +-
 5 files changed, 45 insertions(+), 28 deletions(-)

diff --git a/modules/nf-core/pbmarkdup/main.nf b/modules/nf-core/pbmarkdup/main.nf
index 287e887be5eb..20da004d21b5 100644
--- a/modules/nf-core/pbmarkdup/main.nf
+++ b/modules/nf-core/pbmarkdup/main.nf
@@ -13,7 +13,7 @@ process PBMARKDUP {
     output:
     tuple val(meta), path("${prefix}.${suffix}"), emit: markduped
     tuple val(meta), path("${dupfile_name}")    , emit: dupfile   , optional: true
-    tuple val(meta), path("*.pbmarkdup.log")    , emit: logs      , optional: true
+    tuple val(meta), path("*.pbmarkdup.log")    , emit: log       , optional: true
     path "versions.yml"                         , emit: versions
 
     when:
@@ -28,15 +28,15 @@ process PBMARKDUP {
     def file_list = input.collect { it.getName() }.join(' ')
 
     // Check file name collisions between input, output, and duplicate file
-    if (file_list.contains("${prefix}.${suffix}")) 
+    if (file_list.contains("${prefix}.${suffix}"))
         error """Output file `${prefix}.${suffix}` conflicts with an input file.
         Please change the output `$prefix` or input file names."""
     if (dupfile_name) {
-        if (file_list.contains(dupfile_name)) 
+        if (file_list.contains(dupfile_name))
             error """Duplicate file `$dupfile_name` conflicts with an input file.
             Please change the duplicate file name `$dupfile_name` or input file names."""
 
-        if (dupfile_name == "${prefix}.${suffix}") 
+        if (dupfile_name == "${prefix}.${suffix}")
             error """Duplicate file `$dupfile_name` cannot be the same as the output file name.
             Please change the duplicate file name `$dupfile_name` or output prefix `$prefix`."""
     }
diff --git a/modules/nf-core/pbmarkdup/meta.yml b/modules/nf-core/pbmarkdup/meta.yml
index 7762b0d78b14..9ec66e32929c 100644
--- a/modules/nf-core/pbmarkdup/meta.yml
+++ b/modules/nf-core/pbmarkdup/meta.yml
@@ -49,6 +49,33 @@ output:
             - edam: http://edamontology.org/format_2546 # FASTA-like
             - edam: "http://edamontology.org/format_1930" # FASTQ
             - edam: "http://edamontology.org/format_2572" # BAM
+  dupfile:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${dupfile_name}:
+          type: file
+          description: |
+            (Optional) File listing duplicate reads (Specify by --dup-file).
+          pattern: "*.{bam,f*a,/.*f.*\\.gz/}"
+          ontologies:
+            - edam: http://edamontology.org/format_2546 # FASTA-like
+            - edam: "http://edamontology.org/format_1930" # FASTQ
+            - edam: "http://edamontology.org/format_2572" # BAM
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.pbmarkdup.log":
+          type: file
+          description: |
+            Log file generated by pbmarkdup (if --log-level is specified).
+          pattern: "*.pbmarkdup.log"
+          ontologies: []
   versions:
     - versions.yml:
         type: file
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
index 34d19a058837..70aae1b97b0b 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
         when {
 
             params {
-                pbmarkdup_args = "--clobber --dup-file output.dup.fasta"
+                pbmarkdup_args = "--clobber"
             }
 
             process {
@@ -53,7 +53,7 @@ nextflow_process {
                     [
                         [ id:'test' ], // meta map
                         [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
-                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true) 
+                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
                         ]
                     ]
                 )
@@ -83,7 +83,7 @@ nextflow_process {
                     [
                         [ id:'test' ], // meta map
                         [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
-                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true) 
+                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
                         ]
                     ]
                 )
diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test.snap b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
index 31ae76263b3a..705b7dd4f2ac 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
                 "dupfile": [
                     
                 ],
-                "logs": [
+                "log": [
                     
                 ],
                 "markduped": [
@@ -42,7 +42,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-27T22:01:01.517309"
+        "timestamp": "2025-11-27T22:25:53.428359"
     },
     "acropora cervicornis - bam - multiple tests with dupfile and log": {
         "content": [
@@ -82,7 +82,7 @@
                         "null.dup.bam:md5,3b74225ad5f7e9e1cbafc45132ad82fb"
                     ]
                 ],
-                "logs": [
+                "log": [
                     [
                         {
                             "id": "test"
@@ -107,7 +107,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-27T22:00:33.750177"
+        "timestamp": "2025-11-27T22:25:23.374664"
     },
     "deilephila porcellus - stub": {
         "content": [
@@ -132,7 +132,7 @@
                 "dupfile": [
                     
                 ],
-                "logs": [
+                "log": [
                     
                 ],
                 "markduped": [
@@ -152,7 +152,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-27T22:01:14.242019"
+        "timestamp": "2025-11-27T22:26:16.491708"
     },
     "deilephila porcellus - fasta": {
         "content": [
@@ -166,12 +166,7 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "output.dup.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
                     
@@ -180,14 +175,9 @@
                     "versions.yml:md5,832e36b56615fb29a94b16e4db32b8db"
                 ],
                 "dupfile": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "output.dup.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
-                "logs": [
+                "log": [
                     
                 ],
                 "markduped": [
@@ -207,6 +197,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-11-27T22:00:02.071951"
+        "timestamp": "2025-11-27T22:47:33.595865"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pbmarkdup/tests/nextflow.config b/modules/nf-core/pbmarkdup/tests/nextflow.config
index 38bce1a3ac67..dc9b092f0130 100644
--- a/modules/nf-core/pbmarkdup/tests/nextflow.config
+++ b/modules/nf-core/pbmarkdup/tests/nextflow.config
@@ -2,4 +2,4 @@ process {
     withName: PBMARKDUP {
         ext.args = { "${params.pbmarkdup_args}" }
     }
-}
\ No newline at end of file
+}

From 2a92fde49d9157a9e0ebb9f82bcb3fcb80606e04 Mon Sep 17 00:00:00 2001
From: sainsachiko <hthhanh.work@gmail.com>
Date: Thu, 27 Nov 2025 23:24:17 +0700
Subject: [PATCH 6/8] Update path to test data

---
 modules/nf-core/pbmarkdup/tests/main.nf.test | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/pbmarkdup/tests/main.nf.test b/modules/nf-core/pbmarkdup/tests/main.nf.test
index 70aae1b97b0b..dbe78c3517cc 100644
--- a/modules/nf-core/pbmarkdup/tests/main.nf.test
+++ b/modules/nf-core/pbmarkdup/tests/main.nf.test
@@ -52,8 +52,8 @@ nextflow_process {
                 input[0] = Channel.of(
                     [
                         [ id:'test' ], // meta map
-                        [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
-                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
+                        [ file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
+                          file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
                         ]
                     ]
                 )
@@ -82,8 +82,8 @@ nextflow_process {
                 input[0] = Channel.of(
                     [
                         [ id:'test' ], // meta map
-                        [ file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
-                          file('https://github.com/sainsachiko/test-datasets/raw/refs/heads/modules/data/genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
+                        [ file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.1.bam', checkIfExists: true),
+                          file(params.modules_testdata_base_path + 'genomics/eukaryotes/acropora_cervicornis/m84093_241116_151316_s2.hifi_reads.bc2028.subset.2.bam', checkIfExists: true)
                         ]
                     ]
                 )

From 2d42b4c1b2bf7d74ab5935e14945d2c8a869f4f9 Mon Sep 17 00:00:00 2001
From: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com>
Date: Mon, 1 Dec 2025 14:15:24 +0700
Subject: [PATCH 7/8] Update modules/nf-core/pbmarkdup/meta.yml

---
 modules/nf-core/pbmarkdup/meta.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/pbmarkdup/meta.yml b/modules/nf-core/pbmarkdup/meta.yml
index 9ec66e32929c..fc12076aa073 100644
--- a/modules/nf-core/pbmarkdup/meta.yml
+++ b/modules/nf-core/pbmarkdup/meta.yml
@@ -12,7 +12,8 @@ tools:
   - pbmarkdup:
       description: |
         pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters
-        highly similar CCS reads to detect PCR duplicates and flags them in the BAM output
+        highly similar CCS reads to detect PCR duplicates and flags them in the output files 
+        (BAM,FASTQ,FASTA) (duplicate bit 0x400), optionally removing duplicates.
         (duplicate bit 0x400), optionally removing duplicates.
       homepage: https://github.com/PacificBiosciences/pbmarkdup
       documentation: https://github.com/PacificBiosciences/pbmarkdup

From dc0047b4df9467f3e8d6b8bc4f711623df97c605 Mon Sep 17 00:00:00 2001
From: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com>
Date: Mon, 1 Dec 2025 14:21:49 +0700
Subject: [PATCH 8/8] Fix linting

---
 modules/nf-core/pbmarkdup/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/pbmarkdup/meta.yml b/modules/nf-core/pbmarkdup/meta.yml
index fc12076aa073..59a1de054258 100644
--- a/modules/nf-core/pbmarkdup/meta.yml
+++ b/modules/nf-core/pbmarkdup/meta.yml
@@ -12,7 +12,7 @@ tools:
   - pbmarkdup:
       description: |
         pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters
-        highly similar CCS reads to detect PCR duplicates and flags them in the output files 
+        highly similar CCS reads to detect PCR duplicates and flags them in the output files
         (BAM,FASTQ,FASTA) (duplicate bit 0x400), optionally removing duplicates.
         (duplicate bit 0x400), optionally removing duplicates.
       homepage: https://github.com/PacificBiosciences/pbmarkdup