Generate metadata CSV/TSV in modules instead of workflow body

conf/modules.config

@@ -144,6 +144,20 @@ process {
     // SUBMISSION AND MANIFEST GENERATION
     //
 
+    withName: 'CREATE_ASSEMBLY_METADATA_CSV|CREATE_GENOME_METADATA_TSV' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: 'CONCAT_METADATA|CONCAT_ACCESSIONS' {
+        publishDir = [
+            path: { "${params.outdir}/${params.mode}/upload" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'GENOME_UPLOAD' {
         ext.args = "--force" // ensures that ENA metadata is re-downloaded even if cache exists
         publishDir = [

docs/output.md

@@ -18,7 +18,8 @@ When `--mode mags` or `--mode bins` is used, results are written under `mags/` o
 <summary>Output files</summary>
 
 - `<mode>/`
-  - `genomes_metadata.csv`: tabular metadata assembled for submission.
+  - `upload/assigned_accessions.tsv`: accessions assigned to submitted genomes.
+  - `upload/genomes_metadata.tsv`: tabular metadata gathered for submission.
   - `upload/manifests/`: manifests generated by `genome_uploader`.
   - `databases/checkm2/`: downloaded CheckM2 database file (when downloaded during the run).
   - `databases/cat_pack/`: prepared CAT_pack database directories (when generated during the run).
@@ -41,7 +42,8 @@ When `--mode metagenomic_assemblies` is used, results are written under `metagen
 <summary>Output files</summary>
 
 - `metagenomic_assemblies/`
-  - `<sample>_assembly_metadata.csv`: per-assembly metadata CSV generated for manifest creation.
+  - `upload/assigned_accessions.tsv`: accessions assigned to submitted assemblies.
+  - `upload/assemblies_metadata.csv`: metadata CSV generated for manifest creation.
   - `<sample>/coverage/`: `coverm contig` output for samples where `coverage` had to be calculated from reads.
 
 </details>

modules.json

@@ -66,6 +66,12 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastavalidator/fastavalidator.diff"
                     },
+                    "find/concatenate": {
+                        "branch": "master",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/find/concatenate/find-concatenate.diff"
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",

modules/local/create_assembly_metadata_csv/environment.yml

@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::bash=5.2.37

modules/local/create_assembly_metadata_csv/main.nf

@@ -0,0 +1,51 @@
+process CREATE_ASSEMBLY_METADATA_CSV {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/bash:5.2.26' :
+        'community.wave.seqera.io/library/bash:5.2.37--ae00789afb795adf' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("${meta.id}_assembly_metadata.csv"), emit: csv
+    path "versions.yml"                                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def header = 'Runs,Coverage,Assembler,Version,Filepath,Sample'
+    def row = [
+        meta.run_accession,
+        meta.coverage,
+        meta.assembler,
+        meta.assembler_version,
+        fasta.name,
+        ''    // Sample column left empty because co-assemblies are not supported
+    ].join(',')
+    """
+    cat <<-END_CSV > ${meta.id}_assembly_metadata.csv
+    ${header}
+    ${row}
+    END_CSV
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${meta.id}_assembly_metadata.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
+    END_VERSIONS
+    """
+}

modules/local/create_assembly_metadata_csv/meta.yml

@@ -0,0 +1,48 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "create_assembly_metadata_csv"
+description: Create input CSV metadata file for assembly_uploader tool
+keywords:
+  - assembly
+  - metadata
+  - ena
+  - submission
+tools:
+  - bash:
+      description: Bash shell scripting
+      homepage: https://www.gnu.org/software/bash/
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information:
+          - id: Sample identifier
+          - run_accession: ENA run accession
+          - coverage: Assembly coverage value
+          - assembler: Name of the assembler used
+          - assembler_version: Version of the assembler
+    - fasta:
+        type: file
+        description: Assembly FASTA file
+        pattern: "*.{fasta,fa,fna}"
+
+output:
+  - csv:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information (same as input)
+      - "*.csv":
+          type: file
+          description: CSV file containing assembly metadata to be used as input for the assembly_uploader
+          pattern: "*_assembly_metadata.csv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@ochkalova"
+maintainers:
+  - "@ochkalova"

modules/local/create_assembly_metadata_csv/tests/main.nf.test

@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process CREATE_ASSEMBLY_METADATA_CSV"
+    script "../main.nf"
+    process "CREATE_ASSEMBLY_METADATA_CSV"
+
+    tag "modules"
+    tag "modules_local"
+    tag "create_assembly_metadata_csv"
+
+    test("test_create_assembly_metadata_csv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [
+                        id: 'test_sample',
+                        run_accession: 'ERR123456',
+                        coverage: 50.5,
+                        assembler: 'metaspades',
+                        assembler_version: '3.15.5'
+                    ],
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz')
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("test_create_assembly_metadata_csv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [
+                        id: 'stub_sample',
+                        run_accession: 'ERR999999',
+                        coverage: 75.0,
+                        assembler: 'megahit',
+                        assembler_version: '1.2.9'
+                    ],
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz')
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap

@@ -0,0 +1,84 @@
+{
+    "test_create_assembly_metadata_csv": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_sample",
+                            "run_accession": "ERR123456",
+                            "coverage": 50.5,
+                            "assembler": "metaspades",
+                            "assembler_version": "3.15.5"
+                        },
+                        "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "test_sample",
+                            "run_accession": "ERR123456",
+                            "coverage": 50.5,
+                            "assembler": "metaspades",
+                            "assembler_version": "3.15.5"
+                        },
+                        "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.1"
+        },
+        "timestamp": "2026-04-27T14:51:27.130061"
+    },
+    "test_create_assembly_metadata_csv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "stub_sample",
+                            "run_accession": "ERR999999",
+                            "coverage": 75.0,
+                            "assembler": "megahit",
+                            "assembler_version": "1.2.9"
+                        },
+                        "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "stub_sample",
+                            "run_accession": "ERR999999",
+                            "coverage": 75.0,
+                            "assembler": "megahit",
+                            "assembler_version": "1.2.9"
+                        },
+                        "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.1"
+        },
+        "timestamp": "2026-04-27T14:51:32.249848"
+    }
+}

modules/local/create_genome_metadata_tsv/environment.yml

@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::bash=5.2.37