From bdcf21a1f4ed3b0db4d5f11ad5125fd0302186ff Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Mon, 13 Jul 2026 11:57:45 +0200
Subject: [PATCH 01/11] added gridss assemble module

---
 .../nf-core/gridss/assemble/environment.yml   |   5 +
 modules/nf-core/gridss/assemble/main.nf       |  50 ++++++++
 modules/nf-core/gridss/assemble/meta.yml      | 117 +++++++++++++++++
 .../gridss/assemble/tests/main.nf.test        | 120 ++++++++++++++++++
 4 files changed, 292 insertions(+)
 create mode 100644 modules/nf-core/gridss/assemble/environment.yml
 create mode 100644 modules/nf-core/gridss/assemble/main.nf
 create mode 100644 modules/nf-core/gridss/assemble/meta.yml
 create mode 100644 modules/nf-core/gridss/assemble/tests/main.nf.test

diff --git a/modules/nf-core/gridss/assemble/environment.yml b/modules/nf-core/gridss/assemble/environment.yml
new file mode 100644
index 000000000000..db37d675e605
--- /dev/null
+++ b/modules/nf-core/gridss/assemble/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gridss=2.13.2
diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
new file mode 100644
index 000000000000..c68e680d4cde
--- /dev/null
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -0,0 +1,50 @@
+process GRIDSS_ASSEMBLE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h50ea8bc_3':
+        'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"
+
+    input:
+    tuple val(meta), path(bams), path(bais), path(preprocess_dirs)
+    tuple val(meta2), path(fasta), path(fasta_fai), path(fasta_dict), path(bwa_index)
+    tuple val(meta3), path(gridss_config)
+
+    output:
+    tuple val(meta), path("*.gridss.working"), path("*.sv.assembly.bam"),  emit: assemble_dir
+    tuple val("${task.process}"), val('gridss'), eval("CallVariants --version 2>&1 | sed 's/-gridss//'")  , topic: versions, emit: versions_gridss
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def arg_config = gridss_config ? "-c ${gridss_config}" : ""
+
+    def bams_list = bams instanceof List ? bams : [bams]
+
+    """
+    ln -s \$(find -L ${bwa_index} -regex '.*\\.\\(amb\\|ann\\|pac\\|gridsscache\\|sa\\|bwt\\|img\\|alt\\)') ./
+
+    gridss ${args} \\
+        --jvmheap ${Math.round(task.memory.bytes * 0.95)} \\
+        --steps assemble \\
+        --reference ${fasta} \\
+        --workingdir "." \\
+        --assembly ${prefix}.sv.assembly.bam \\
+        --threads ${task.cpus} ${arg_config} ${bams_list.join(' ')}
+
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}.sv.assembly.bam.gridss.working
+    touch ${prefix}.sv.assembly.bam
+
+    """
+}
diff --git a/modules/nf-core/gridss/assemble/meta.yml b/modules/nf-core/gridss/assemble/meta.yml
new file mode 100644
index 000000000000..3c14c5d4be56
--- /dev/null
+++ b/modules/nf-core/gridss/assemble/meta.yml
@@ -0,0 +1,117 @@
+name: "gridss_assemble"
+description: Assemble breakend contigs for GRIDSS structural variant calling
+keywords:
+  - bam
+  - assembly
+  - structural variants
+  - gridss
+  - breakend
+  - variant calling
+tools:
+  - gridss:
+      description: "GRIDSS: the Genomic Rearrangement IDentification Software Suite"
+      homepage: "https://github.com/PapenfussLab/gridss"
+      documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
+      tool_dev_url: "https://github.com/PapenfussLab/gridss"
+      doi: "10.1186/s13059-021-02423-x"
+      licence:
+        - "GPL v3"
+      identifier: biotools:gridss
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bams:
+        type: file
+        description: Input BAM file(s)
+        pattern: "*.bam"
+        ontologies:
+          - edam: http://edamontology.org/format_2572
+    - bais:
+        type: file
+        description: BAM index file(s)
+        pattern: "*.bam.bai"
+        ontologies: []
+    - preprocess_dirs:
+        type: directory
+        description: GRIDSS preprocessing working directories from the GRIDSS_PREPROCESS step
+        pattern: "*.gridss.working/"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference genome information
+          e.g. `[ id:'genome' ]`
+    - fasta:
+        type: file
+        description: Reference genome FASTA file
+        pattern: "*.{fasta,fa,fna}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929
+    - fasta_fai:
+        type: file
+        description: Reference genome FASTA index file
+        pattern: "*.fai"
+        ontologies: []
+    - fasta_dict:
+        type: file
+        description: Reference genome sequence dictionary
+        pattern: "*.dict"
+        ontologies: []
+    - bwa_index:
+        type: directory
+        description: Directory containing the GRIDSS/BWA index files for the reference genome
+        pattern: "*"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing GRIDSS configuration information
+          e.g. `[ id:'gridss_config' ]`
+    - gridss_config:
+        type: file
+        description: Optional GRIDSS configuration file
+        pattern: "*.{properties,config}"
+        ontologies: []
+output:
+  assemble_dir:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.gridss.working":
+          type: directory
+          description: GRIDSS assembly working directory containing assembled breakend contigs
+          pattern: "*.gridss.working"
+      - "*.sv.assembly.bam":
+          type: file
+          description: BAM file containing the assembled breakend contigs
+          pattern: "*.sv.assembly.bam"
+          ontologies:
+            - edam: http://edamontology.org/format_2572
+  versions_gridss:
+    - - ${task.process}:
+          type: string
+          description: The process
+      - gridss:
+          type: string
+          description: The tool name
+      - CallVariants --version 2>&1 | sed 's/-gridss//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process
+      - gridss:
+          type: string
+          description: The tool name
+      - CallVariants --version 2>&1 | sed 's/-gridss//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@imsarath"
+maintainers:
+  - "@imsarath"
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
new file mode 100644
index 000000000000..19ea9cd3eedb
--- /dev/null
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -0,0 +1,120 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test gridss/assemble
+nextflow_process {
+
+    name "Test Process GRIDSS_ASSEMBLE"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "GRIDSS_ASSEMBLE"
+
+    tag "modules"
+    tag "modules_local"
+    tag "gridss"
+    tag "gridss/assemble"
+
+    setup {
+        run("UNTAR") {
+            script "../../untar/main.nf"
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'gridss_preprocess_dir' ],
+                    file(params.modules_testdata_base_path + 'testdata/gridss/gridss_preprocess_dir.tar.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        run("BWA_INDEX") {
+            script "../../bwa/index/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("gridss_assemble - human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]).join(UNTAR.out.untar)
+                input[1] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                ]).join(BWA_INDEX.out.index)
+                input[2] = channel.of([
+                    [ id: 'gridss_config' ],
+                    file(params.modules_testdata_base_path + 'reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.assemble_dir.collect { meta, working, assembly ->
+                        [meta, file(working).list().sort(), file(assembly).name]
+                    },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
+    test("gridss_assemble - human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'test_sample', sample_type: 'tumor' ],
+                    file(params.modules_testdata_base_path + 'testdata/bam/test.paired_end.markduplicates.gridss.targeted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'testdata/bam/test.paired_end.markduplicates.gridss.targeted.bam.bai', checkIfExists: true)
+                ])
+                .join(UNTAR.out.untar)
+                input[1] = channel.of([
+                    [ id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'testdata/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BWA_INDEX.out.index
+                input[3] = channel.of([
+                    [ id: 'genome_fai' ],
+                    file(params.modules_testdata_base_path + 'testdata/genome/genome.fasta.fai', checkIfExists: true)
+                ])
+                input[4] = channel.of([
+                    [ id: 'genome_dict' ],
+                    file(params.modules_testdata_base_path + 'testdata/genome/genome.dict', checkIfExists: true)
+                ])
+                input[5] = channel.of([
+                    [ id: 'gridss_config' ],
+                    file(params.modules_testdata_base_path + 'reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+}

From 0fd8576201bd92b3634ad2f549eb897b2af5845b Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 17 Jul 2026 14:00:49 +0200
Subject: [PATCH 02/11] fix: input channels in nf-test and stub

---
 modules/nf-core/gridss/assemble/main.nf       | 23 +++++++-
 .../gridss/assemble/tests/main.nf.test        | 52 ++++++++-----------
 2 files changed, 42 insertions(+), 33 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index c68e680d4cde..d4c39a778c83 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -9,7 +9,7 @@ process GRIDSS_ASSEMBLE {
 
     input:
     tuple val(meta), path(bams), path(bais), path(preprocess_dirs)
-    tuple val(meta2), path(fasta), path(fasta_fai), path(fasta_dict), path(bwa_index)
+    tuple val(meta2), path(fasta), path(fasta_fai), path(bwa_index)
     tuple val(meta3), path(gridss_config)
 
     output:
@@ -27,7 +27,14 @@ process GRIDSS_ASSEMBLE {
     def bams_list = bams instanceof List ? bams : [bams]
 
     """
-    ln -s \$(find -L ${bwa_index} -regex '.*\\.\\(amb\\|ann\\|pac\\|gridsscache\\|sa\\|bwt\\|img\\|alt\\)') ./
+    # GRIDSS requires all BWA index files to have the exact
+    # same basename as the reference fasta. This is a hard
+    # requirement of the tool - it will fail to find indices otherwise.
+    index_files=(\$(find -L "${bwa_index}" -regex '.*\\.\\(amb\\|ann\\|pac\\|gridsscache\\|sa\\|bwt\\|img\\|alt\\)\$'))
+
+    for index_file in "\${index_files[@]}"; do
+        ln -sf "\$index_file" "./${fasta}.\${index_file##*.}"
+    done
 
     gridss ${args} \\
         --jvmheap ${Math.round(task.memory.bytes * 0.95)} \\
@@ -44,7 +51,19 @@ process GRIDSS_ASSEMBLE {
 
     """
     mkdir -p ${prefix}.sv.assembly.bam.gridss.working
+
     touch ${prefix}.sv.assembly.bam
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.cigar_metrics",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.coverage.blacklist.bed",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.downsampled_0.bed",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.excluded_0.bed",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.idsv_metrics",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.mapq_metrics",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.quality_distribution_metrics",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.subsetCalled_0.bed",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam.bai",
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.tag_metrics"
 
     """
 }
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
index 19ea9cd3eedb..3746942d0eb3 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_process {
 
     name "Test Process GRIDSS_ASSEMBLE"
     script "../main.nf"
-    config "./nextflow.config"
+    // config "./nextflow.config"
     process "GRIDSS_ASSEMBLE"
 
     tag "modules"
@@ -14,19 +14,19 @@ nextflow_process {
 
     setup {
         run("UNTAR") {
-            script "../../untar/main.nf"
+            script "../../../untar/main.nf"
             process {
                 """
                 input[0] = channel.of([
-                    [ id: 'gridss_preprocess_dir' ],
-                    file(params.modules_testdata_base_path + 'testdata/gridss/gridss_preprocess_dir.tar.gz', checkIfExists: true)
+                    [ id: 'test.paired_end.sorted.bam.gridss.working' ],
+                    file(params.modules_testdata_base_path + 'test.paired_end.sorted.bam.gridss.preprocess.tar.gz', checkIfExists: true)
                 ])
                 """
             }
         }
 
         run("BWA_INDEX") {
-            script "../../bwa/index/main.nf"
+            script "../../../bwa/index/main.nf"
             process {
                 """
                 input[0] = [
@@ -38,7 +38,7 @@ nextflow_process {
         }
     }
 
-    test("gridss_assemble - human - bam") {
+    test("human - bam") {
 
         when {
             process {
@@ -47,16 +47,15 @@ nextflow_process {
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]).join(UNTAR.out.untar)
+                ]).combine(UNTAR.out.untar).map { meta, bam, bai, meta_untar, preprocess_dir -> [meta, bam, bai, preprocess_dir] }
                 input[1] = channel.of([
                     [id:'fasta'],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
-                ]).join(BWA_INDEX.out.index)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).combine(BWA_INDEX.out.index).map { meta, fasta, fai, meta_index, bwa_index -> [meta, fasta, fai, bwa_index] }
                 input[2] = channel.of([
                     [ id: 'gridss_config' ],
-                    file(params.modules_testdata_base_path + 'reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
                 ])
                 """
             }
@@ -75,7 +74,7 @@ nextflow_process {
         }
     }
 
-    test("gridss_assemble - human - bam - stub") {
+    test("human - bam - stub") {
 
         options "-stub"
 
@@ -83,27 +82,18 @@ nextflow_process {
             process {
                 """
                 input[0] = channel.of([
-                    [ id: 'test_sample', sample_type: 'tumor' ],
-                    file(params.modules_testdata_base_path + 'testdata/bam/test.paired_end.markduplicates.gridss.targeted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'testdata/bam/test.paired_end.markduplicates.gridss.targeted.bam.bai', checkIfExists: true)
-                ])
-                .join(UNTAR.out.untar)
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]).combine(UNTAR.out.untar).map { meta, bam, bai, meta_untar, preprocess_dir -> [meta, bam, bai, preprocess_dir] }
                 input[1] = channel.of([
-                    [ id: 'genome' ],
-                    file(params.modules_testdata_base_path + 'testdata/genome/genome.fasta', checkIfExists: true)
-                ])
-                input[2] = BWA_INDEX.out.index
-                input[3] = channel.of([
-                    [ id: 'genome_fai' ],
-                    file(params.modules_testdata_base_path + 'testdata/genome/genome.fasta.fai', checkIfExists: true)
-                ])
-                input[4] = channel.of([
-                    [ id: 'genome_dict' ],
-                    file(params.modules_testdata_base_path + 'testdata/genome/genome.dict', checkIfExists: true)
-                ])
-                input[5] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).combine(BWA_INDEX.out.index).map { meta, fasta, fai, meta_index, bwa_index -> [meta, fasta, fai, bwa_index] }
+                input[2] = channel.of([
                     [ id: 'gridss_config' ],
-                    file(params.modules_testdata_base_path + 'reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
                 ])
                 """
             }

From 54469aadff4cb144836a070f58baaa10a506bb47 Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Wed, 22 Jul 2026 10:27:26 +0200
Subject: [PATCH 03/11] fix: nf-test gridss assemble

---
 .../gridss/assemble/tests/main.nf.test        | 37 +++++++++--------
 .../gridss/assemble/tests/main.nf.test.snap   | 41 +++++++++++++++++++
 2 files changed, 61 insertions(+), 17 deletions(-)
 create mode 100644 modules/nf-core/gridss/assemble/tests/main.nf.test.snap

diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
index 3746942d0eb3..8707fbb7cf1b 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -1,10 +1,7 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test gridss/assemble
 nextflow_process {
 
     name "Test Process GRIDSS_ASSEMBLE"
     script "../main.nf"
-    // config "./nextflow.config"
     process "GRIDSS_ASSEMBLE"
 
     tag "modules"
@@ -13,26 +10,32 @@ nextflow_process {
     tag "gridss/assemble"
 
     setup {
-        run("UNTAR") {
-            script "../../../untar/main.nf"
+        run("BWA_INDEX") {
+            script "../../../bwa/index/main.nf"
             process {
                 """
-                input[0] = channel.of([
-                    [ id: 'test.paired_end.sorted.bam.gridss.working' ],
-                    file(params.modules_testdata_base_path + 'test.paired_end.sorted.bam.gridss.preprocess.tar.gz', checkIfExists: true)
-                ])
+                input[0] = [
+                    [ id: 'fasta' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
                 """
             }
         }
 
-        run("BWA_INDEX") {
-            script "../../../bwa/index/main.nf"
+        run("GRIDSS_PREPROCESS") {
+            script "../../preprocess/main.nf"
             process {
                 """
                 input[0] = [
-                    [ id: 'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
+                input[1] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).join(BWA_INDEX.out.index)
                 """
             }
         }
@@ -47,12 +50,12 @@ nextflow_process {
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]).combine(UNTAR.out.untar).map { meta, bam, bai, meta_untar, preprocess_dir -> [meta, bam, bai, preprocess_dir] }
+                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
                 input[1] = channel.of([
                     [id:'fasta'],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]).combine(BWA_INDEX.out.index).map { meta, fasta, fai, meta_index, bwa_index -> [meta, fasta, fai, bwa_index] }
+                ]).join(BWA_INDEX.out.index)
                 input[2] = channel.of([
                     [ id: 'gridss_config' ],
                     file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
@@ -85,12 +88,12 @@ nextflow_process {
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]).combine(UNTAR.out.untar).map { meta, bam, bai, meta_untar, preprocess_dir -> [meta, bam, bai, preprocess_dir] }
+                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
                 input[1] = channel.of([
                     [id:'fasta'],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]).combine(BWA_INDEX.out.index).map { meta, fasta, fai, meta_index, bwa_index -> [meta, fasta, fai, bwa_index] }
+                ]).join(BWA_INDEX.out.index)
                 input[2] = channel.of([
                     [ id: 'gridss_config' ],
                     file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test.snap b/modules/nf-core/gridss/assemble/tests/main.nf.test.snap
new file mode 100644
index 000000000000..43b5fc2ed922
--- /dev/null
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+    "human - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "test.sv.assembly.bam.cigar_metrics",
+                        "test.sv.assembly.bam.coverage.blacklist.bed",
+                        "test.sv.assembly.bam.downsampled_0.bed",
+                        "test.sv.assembly.bam.excluded_0.bed",
+                        "test.sv.assembly.bam.idsv_metrics",
+                        "test.sv.assembly.bam.mapq_metrics",
+                        "test.sv.assembly.bam.quality_distribution_metrics",
+                        "test.sv.assembly.bam.subsetCalled_0.bed",
+                        "test.sv.assembly.bam.sv.bam",
+                        "test.sv.assembly.bam.sv.bam.bai",
+                        "test.sv.assembly.bam.tag_metrics"
+                    ],
+                    "test.sv.assembly.bam"
+                ]
+            ],
+            {
+                "versions_gridss": [
+                    [
+                        "GRIDSS_ASSEMBLE",
+                        "gridss",
+                        "2.13.2"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-22T10:14:13.072385086",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "26.04.3"
+        }
+    }
+}
\ No newline at end of file

From 136e4942571b3ddc91b3a3d103d9c12c334a9420 Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 10:41:11 +0200
Subject: [PATCH 04/11] update the nf-test snapshot

---
 modules/nf-core/gridss/assemble/main.nf       |  22 ++--
 .../gridss/assemble/tests/main.nf.test        | 113 ------------------
 .../gridss/assemble/tests/main.nf.test.snap   |  41 ++++++-
 3 files changed, 51 insertions(+), 125 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index d4c39a778c83..e1d32157d825 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -53,17 +53,17 @@ process GRIDSS_ASSEMBLE {
     mkdir -p ${prefix}.sv.assembly.bam.gridss.working
 
     touch ${prefix}.sv.assembly.bam
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.cigar_metrics",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.coverage.blacklist.bed",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.downsampled_0.bed",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.excluded_0.bed",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.idsv_metrics",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.mapq_metrics",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.quality_distribution_metrics",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.subsetCalled_0.bed",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam.bai",
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.tag_metrics"
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.cigar_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.coverage.blacklist.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.downsampled_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.excluded_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.idsv_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.mapq_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.quality_distribution_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.subsetCalled_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam.bai
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.tag_metrics
 
     """
 }
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
index 8707fbb7cf1b..e69de29bb2d1 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -1,113 +0,0 @@
-nextflow_process {
-
-    name "Test Process GRIDSS_ASSEMBLE"
-    script "../main.nf"
-    process "GRIDSS_ASSEMBLE"
-
-    tag "modules"
-    tag "modules_local"
-    tag "gridss"
-    tag "gridss/assemble"
-
-    setup {
-        run("BWA_INDEX") {
-            script "../../../bwa/index/main.nf"
-            process {
-                """
-                input[0] = [
-                    [ id: 'fasta' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        run("GRIDSS_PREPROCESS") {
-            script "../../preprocess/main.nf"
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]
-                input[1] = channel.of([
-                    [id:'fasta'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]).join(BWA_INDEX.out.index)
-                """
-            }
-        }
-    }
-
-    test("human - bam") {
-
-        when {
-            process {
-                """
-                input[0] = channel.of([
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
-                input[1] = channel.of([
-                    [id:'fasta'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]).join(BWA_INDEX.out.index)
-                input[2] = channel.of([
-                    [ id: 'gridss_config' ],
-                    file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.assemble_dir.collect { meta, working, assembly ->
-                        [meta, file(working).list().sort(), file(assembly).name]
-                    },
-                    process.out.findAll { key, val -> key.startsWith("versions") }
-                ).match() }
-            )
-        }
-    }
-
-    test("human - bam - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = channel.of([
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
-                input[1] = channel.of([
-                    [id:'fasta'],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]).join(BWA_INDEX.out.index)
-                input[2] = channel.of([
-                    [ id: 'gridss_config' ],
-                    file(params.modules_testdata_base_path + 'test-data/reference/GRCh37/gridss/gridss.properties', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
-            )
-        }
-    }
-
-}
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test.snap b/modules/nf-core/gridss/assemble/tests/main.nf.test.snap
index 43b5fc2ed922..07ca355bb3e9 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test.snap
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test.snap
@@ -1,4 +1,43 @@
 {
+    "human - bam - stub": {
+        "content": [
+            {
+                "assemble_dir": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.sv.assembly.bam.cigar_metrics:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.coverage.blacklist.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.downsampled_0.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.excluded_0.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.idsv_metrics:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.mapq_metrics:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.subsetCalled_0.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.sv.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.sv.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sv.assembly.bam.tag_metrics:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ],
+                        "test.sv.assembly.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_gridss": [
+                    [
+                        "GRIDSS_ASSEMBLE",
+                        "gridss",
+                        "2.13.2"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-24T10:34:32.103764795",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "26.04.3"
+        }
+    },
     "human - bam": {
         "content": [
             [
@@ -32,7 +71,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-22T10:14:13.072385086",
+        "timestamp": "2026-07-24T10:34:17.884396972",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "26.04.3"

From fe77aad165a9c807a452cba4b29039b83be36bfd Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 10:49:50 +0200
Subject: [PATCH 05/11] fix: assemble main.nf-test

---
 modules/nf-core/gridss/assemble/meta.yml      |  14 +--
 .../gridss/assemble/tests/main.nf.test        | 113 ++++++++++++++++++
 2 files changed, 119 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/meta.yml b/modules/nf-core/gridss/assemble/meta.yml
index 3c14c5d4be56..3e66908644e4 100644
--- a/modules/nf-core/gridss/assemble/meta.yml
+++ b/modules/nf-core/gridss/assemble/meta.yml
@@ -36,7 +36,8 @@ input:
         ontologies: []
     - preprocess_dirs:
         type: directory
-        description: GRIDSS preprocessing working directories from the GRIDSS_PREPROCESS step
+        description: GRIDSS preprocessing working directories from the
+          GRIDSS_PREPROCESS step
         pattern: "*.gridss.working/"
   - - meta2:
         type: map
@@ -54,14 +55,10 @@ input:
         description: Reference genome FASTA index file
         pattern: "*.fai"
         ontologies: []
-    - fasta_dict:
-        type: file
-        description: Reference genome sequence dictionary
-        pattern: "*.dict"
-        ontologies: []
     - bwa_index:
         type: directory
-        description: Directory containing the GRIDSS/BWA index files for the reference genome
+        description: Directory containing the GRIDSS/BWA index files for the
+          reference genome
         pattern: "*"
   - - meta3:
         type: map
@@ -82,7 +79,8 @@ output:
             e.g. `[ id:'sample1' ]`
       - "*.gridss.working":
           type: directory
-          description: GRIDSS assembly working directory containing assembled breakend contigs
+          description: GRIDSS assembly working directory containing assembled
+            breakend contigs
           pattern: "*.gridss.working"
       - "*.sv.assembly.bam":
           type: file
diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
index e69de29bb2d1..1d9f1b91ff25 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -0,0 +1,113 @@
+nextflow_process {
+
+    name "Test Process GRIDSS_ASSEMBLE"
+    script "../main.nf"
+    process "GRIDSS_ASSEMBLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gridss"
+    tag "gridss/assemble"
+
+    setup {
+        run("BWA_INDEX") {
+            script "../../../bwa/index/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'fasta' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        run("GRIDSS_PREPROCESS") {
+            script "../../preprocess/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).join(BWA_INDEX.out.index)
+                """
+            }
+        }
+    }
+
+    test("human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
+                input[1] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).join(BWA_INDEX.out.index)
+                input[2] = channel.of([
+                    [id:'gridss_config'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gridss/gridss.properties', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.assemble_dir.collect { meta, working, assembly ->
+                        [meta, file(working).list().sort(), file(assembly).name]
+                    },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]).join(GRIDSS_PREPROCESS.out.preprocess_dir)
+                input[1] = channel.of([
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]).join(BWA_INDEX.out.index)
+                input[2] = channel.of([
+                    [id:'gridss_config'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gridss/gridss.properties', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+}

From 1057c424033ca439e2c22f2d41bbc90d449066b8 Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 10:56:19 +0200
Subject: [PATCH 06/11] fix: nf-core modules lint issue

---
 modules/nf-core/gridss/assemble/tests/main.nf.test | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/gridss/assemble/tests/main.nf.test b/modules/nf-core/gridss/assemble/tests/main.nf.test
index 1d9f1b91ff25..c11aa76b978f 100644
--- a/modules/nf-core/gridss/assemble/tests/main.nf.test
+++ b/modules/nf-core/gridss/assemble/tests/main.nf.test
@@ -6,7 +6,9 @@ nextflow_process {
 
     tag "modules"
     tag "modules_nfcore"
+    tag "bwa/index"
     tag "gridss"
+    tag "gridss/preprocess"
     tag "gridss/assemble"
 
     setup {

From 76a44e6a9dd569c7073bf8a789d06d66dfc36e3c Mon Sep 17 00:00:00 2001
From: Sarath Kumar Murugan <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 11:26:17 +0200
Subject: [PATCH 07/11] Update modules/nf-core/gridss/assemble/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 modules/nf-core/gridss/assemble/main.nf | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index e1d32157d825..c444f35ce7da 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -25,16 +25,11 @@ process GRIDSS_ASSEMBLE {
     def arg_config = gridss_config ? "-c ${gridss_config}" : ""
 
     def bams_list = bams instanceof List ? bams : [bams]
-
-    """
-    # GRIDSS requires all BWA index files to have the exact
-    # same basename as the reference fasta. This is a hard
-    # requirement of the tool - it will fail to find indices otherwise.
-    index_files=(\$(find -L "${bwa_index}" -regex '.*\\.\\(amb\\|ann\\|pac\\|gridsscache\\|sa\\|bwt\\|img\\|alt\\)\$'))
-
-    for index_file in "\${index_files[@]}"; do
-        ln -sf "\$index_file" "./${fasta}.\${index_file##*.}"
-    done
+	def index_files = bwa_index instanceof List ? bwa_index : [bwa_index]
+	// GRIDSS requires all BWA index files to have the exact same basename as the reference fasta 
+	def link_cmds = index_files.collect { idx -> "ln -sf ${idx} ./${fasta}.${idx.extension}" }.join('\n')
+	"""
+	${link_cmds}
 
     gridss ${args} \\
         --jvmheap ${Math.round(task.memory.bytes * 0.95)} \\

From f3fcfa3e2f83c5eec1577625193dd209f4fba2ed Mon Sep 17 00:00:00 2001
From: Sarath Kumar Murugan <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 11:26:31 +0200
Subject: [PATCH 08/11] Update modules/nf-core/gridss/assemble/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 modules/nf-core/gridss/assemble/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index c444f35ce7da..d44004c7ea0f 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -37,7 +37,9 @@ process GRIDSS_ASSEMBLE {
         --reference ${fasta} \\
         --workingdir "." \\
         --assembly ${prefix}.sv.assembly.bam \\
-        --threads ${task.cpus} ${arg_config} ${bams_list.join(' ')}
+        --threads ${task.cpus} \\
+        ${arg_config} \\
+        ${bams_list.join(' ')}
 
     """
 

From 4324d8be4db71846d7ba553205096999a32163a7 Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 11:32:34 +0200
Subject: [PATCH 09/11]  applied suggestions

---
 modules/nf-core/gridss/assemble/main.nf | 66 -------------------------
 1 file changed, 66 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index d44004c7ea0f..e69de29bb2d1 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -1,66 +0,0 @@
-process GRIDSS_ASSEMBLE {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h50ea8bc_3':
-        'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"
-
-    input:
-    tuple val(meta), path(bams), path(bais), path(preprocess_dirs)
-    tuple val(meta2), path(fasta), path(fasta_fai), path(bwa_index)
-    tuple val(meta3), path(gridss_config)
-
-    output:
-    tuple val(meta), path("*.gridss.working"), path("*.sv.assembly.bam"),  emit: assemble_dir
-    tuple val("${task.process}"), val('gridss'), eval("CallVariants --version 2>&1 | sed 's/-gridss//'")  , topic: versions, emit: versions_gridss
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def arg_config = gridss_config ? "-c ${gridss_config}" : ""
-
-    def bams_list = bams instanceof List ? bams : [bams]
-	def index_files = bwa_index instanceof List ? bwa_index : [bwa_index]
-	// GRIDSS requires all BWA index files to have the exact same basename as the reference fasta 
-	def link_cmds = index_files.collect { idx -> "ln -sf ${idx} ./${fasta}.${idx.extension}" }.join('\n')
-	"""
-	${link_cmds}
-
-    gridss ${args} \\
-        --jvmheap ${Math.round(task.memory.bytes * 0.95)} \\
-        --steps assemble \\
-        --reference ${fasta} \\
-        --workingdir "." \\
-        --assembly ${prefix}.sv.assembly.bam \\
-        --threads ${task.cpus} \\
-        ${arg_config} \\
-        ${bams_list.join(' ')}
-
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    """
-    mkdir -p ${prefix}.sv.assembly.bam.gridss.working
-
-    touch ${prefix}.sv.assembly.bam
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.cigar_metrics
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.coverage.blacklist.bed
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.downsampled_0.bed
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.excluded_0.bed
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.idsv_metrics
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.mapq_metrics
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.quality_distribution_metrics
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.subsetCalled_0.bed
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam.bai
-    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.tag_metrics
-
-    """
-}

From ea5681a2a966a95fd1b86147dc90bd1a86da8c89 Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 11:39:01 +0200
Subject: [PATCH 10/11] fix: updated main.nf

---
 modules/nf-core/gridss/assemble/main.nf | 66 +++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

diff --git a/modules/nf-core/gridss/assemble/main.nf b/modules/nf-core/gridss/assemble/main.nf
index e69de29bb2d1..88e8602781ca 100644
--- a/modules/nf-core/gridss/assemble/main.nf
+++ b/modules/nf-core/gridss/assemble/main.nf
@@ -0,0 +1,66 @@
+process GRIDSS_ASSEMBLE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h50ea8bc_3':
+        'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(preprocess_dir)
+    tuple val(meta2), path(fasta), path(fasta_fai), path(bwa_index)
+    tuple val(meta3), path(gridss_config)
+
+    output:
+    tuple val(meta), path("*.gridss.working"), path("*.sv.assembly.bam"),  emit: assemble_dir
+    tuple val("${task.process}"), val('gridss'), eval("CallVariants --version 2>&1 | sed 's/-gridss//'")  , topic: versions, emit: versions_gridss
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def arg_config = gridss_config ? "-c ${gridss_config}" : ""
+
+    def bam_list = bam instanceof List ? bam : [bam]
+	def index_files = bwa_index instanceof List ? bwa_index : [bwa_index]
+	// GRIDSS requires all BWA index files to have the exact same basename as the reference fasta
+	def link_cmds = index_files.collect { idx -> "ln -sf ${idx} ./${fasta}.${idx.extension}" }.join('\n')
+	"""
+	${link_cmds}
+
+    gridss ${args} \\
+        --jvmheap ${Math.round(task.memory.bytes * 0.95)} \\
+        --steps assemble \\
+        --reference ${fasta} \\
+        --workingdir "." \\
+        --assembly ${prefix}.sv.assembly.bam \\
+        --threads ${task.cpus} \\
+        ${arg_config} \\
+        ${bam_list.join(' ')}
+
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}.sv.assembly.bam.gridss.working
+
+    touch ${prefix}.sv.assembly.bam
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.cigar_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.coverage.blacklist.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.downsampled_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.excluded_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.idsv_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.mapq_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.quality_distribution_metrics
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.subsetCalled_0.bed
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.sv.bam.bai
+    touch ${prefix}.sv.assembly.bam.gridss.working/${prefix}.sv.assembly.bam.tag_metrics
+
+    """
+}

From 702cfb48cff295ad4b6f73e5595e250f1b82d0de Mon Sep 17 00:00:00 2001
From: imsarath <sarath.murugan@outlook.com>
Date: Fri, 24 Jul 2026 11:44:28 +0200
Subject: [PATCH 11/11] fix: nf-core modules linting

---
 modules/nf-core/gridss/assemble/meta.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/gridss/assemble/meta.yml b/modules/nf-core/gridss/assemble/meta.yml
index 3e66908644e4..923ca80f52f5 100644
--- a/modules/nf-core/gridss/assemble/meta.yml
+++ b/modules/nf-core/gridss/assemble/meta.yml
@@ -23,18 +23,18 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. `[ id:'sample1' ]`
-    - bams:
+    - bam:
         type: file
         description: Input BAM file(s)
         pattern: "*.bam"
         ontologies:
           - edam: http://edamontology.org/format_2572
-    - bais:
+    - bai:
         type: file
         description: BAM index file(s)
         pattern: "*.bam.bai"
         ontologies: []
-    - preprocess_dirs:
+    - preprocess_dir:
         type: directory
         description: GRIDSS preprocessing working directories from the
           GRIDSS_PREPROCESS step