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Merge pull request #12 from nf-core/feature/assembly_manifest
add nf-core style module for assembly_manifest
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‎CHANGELOG.md‎

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@@ -9,6 +9,9 @@ Initial release of nf-core/seqsubmit, created with the [nf-core](https://nf-co.r
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### `Added`
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- [#12](https://github.com/nf-core/seqsubmit/pull/12)
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- Add initial version of `GENERATE_ASSEMBLY_MANIFEST` (by @fxquah)
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- [#2](https://github.com/nf-core/proteinfamilies/pull/2)
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- Added initial versions of local modules for `GENOME_UPLOAD` and `ENA_WEBIN_CLI`. (by @KateSakharova and @vagkaratzas)
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- Added initial version of the `GENOMESUBMIT` workflow. (by @KateSakharova and @vagkaratzas)

‎modules/local/generate_assembly_manifest/environment.yml‎

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---
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::assembly_uploader=1.3.2"

‎modules/local/generate_assembly_manifest/main.nf‎

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process GENERATE_ASSEMBLY_MANIFEST {
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tag "$meta.id"
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label 'process_single'
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container "community.wave.seqera.io/library/pip_assembly-uploader:7e9461afbdd7a521"
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input:
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tuple val(meta), path(assembly_fasta), path(data_csv)
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val(assembly_study)
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output:
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tuple val(meta), path("${assembly_study}_upload/*.manifest") , emit: manifest
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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assembly_manifest \\
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--study ${assembly_study} \\
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--data ${data_csv} \\
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--assembly_study ${assembly_study} \\
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--output ${assembly_study}_upload \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version)
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir ${assembly_study}_upload/
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touch ${assembly_study}_upload/test.manifest
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version)
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END_VERSIONS
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"""
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}

‎modules/local/generate_assembly_manifest/meta.yml‎

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name: "generate_assembly_manifest"
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description: Generate manifest files for genome assemblies using assembly-uploader
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keywords:
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- ena
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- manifest
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- upload
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tools:
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- assembly-uploader:
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description: Make a manifest file for each assembly.
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Co-assemblies cannot be generated from a mix of private and public runs -
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all runs used in a co-assembly must have the same privacy status (all private or all public).
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documentation: https://github.com/EBI-Metagenomics/assembly_uploader/
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licence: ["Apache License"]
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information.
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e.g. [ id:'test', single_end:false ]
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- assembly_fasta:
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type: file
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description: Genome assembly FASTA file.
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- data_csv:
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type: file
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description: |
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CSV file containing metadata -
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runs (comma-separated and in quotes, example: "SRR1234,SRR5678"),
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coverage, assembler, version, filepath and optionally sample.
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- assembly_study:
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type: value
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description: |
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Pre-existing study ID to submit to if available.
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Must exist in the webin account.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information.
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e.g. [ id:'test', single_end:false ]
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- manifest:
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type: file
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description: Manifest file required for submission with webin-cli.
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- versions:
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type: file
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description: File containing software versions.
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pattern: "versions.yml"
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authors:
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- "@fxquah"

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

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nextflow_process {
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name "Test Process GENERATE_ASSEMBLY_MANIFEST"
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script "../main.nf"
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process "GENERATE_ASSEMBLY_MANIFEST"
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tag "modules"
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tag "modules_"
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tag "generate_assembly_manifest"
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test("GENERATE_ASSEMBLY_MANIFEST completes with expected outputs") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.pipelines_testdata_base_path + "/test_data/contigs.fasta.gz", checkIfExists: true),
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file(params.pipelines_testdata_base_path + "/samplesheets/samplesheet_generatemanifest.csv", checkIfExists: true)
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]
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input[1] = "PRJ12345"
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"""
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}
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}
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then {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out,
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path(process.out.versions[0]).yaml
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).match() },
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{ assert process.out.manifest.size() == 1 },
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{ assert process.out.manifest[0][1].toString().endsWith(".manifest") },
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{
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def manifestContent = path(process.out.manifest[0][1]).text
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assert manifestContent.contains("PRJ12345") : "PRJ12345 not found in manifest file"
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}
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)
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}
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}
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test("GENERATE_ASSEMBLY_MANIFEST completes with expected outputs - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file('test_contigs.fastq.gz'),
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file('test_samplesheet_generatemanifest.csv')
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]
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input[1] = "PRJ12345"
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"""
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}
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}
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then {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out,
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path(process.out.versions[0]).yaml
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).match() }
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)
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}
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}
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}

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

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{
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"GENERATE_ASSEMBLY_MANIFEST completes with expected outputs - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.manifest:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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"versions.yml:md5,188d7f56d019104ee5883d69eede27b4"
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],
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"manifest": [
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[
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{
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"id": "test"
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},
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"test.manifest:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,188d7f56d019104ee5883d69eede27b4"
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]
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},
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{
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"GENERATE_ASSEMBLY_MANIFEST": {
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"python": "Python 3.14.0"
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}
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-10-29T11:00:23.072784"
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},
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"GENERATE_ASSEMBLY_MANIFEST completes with expected outputs": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"233126d4c4d023f18c7836ed36395e3c.manifest:md5,b31fec00db575da44ad17950ae2e37ff"
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]
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],
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"1": [
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"versions.yml:md5,188d7f56d019104ee5883d69eede27b4"
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],
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"manifest": [
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[
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{
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"id": "test"
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},
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"233126d4c4d023f18c7836ed36395e3c.manifest:md5,b31fec00db575da44ad17950ae2e37ff"
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]
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],
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"versions": [
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"versions.yml:md5,188d7f56d019104ee5883d69eede27b4"
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]
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},
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{
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"GENERATE_ASSEMBLY_MANIFEST": {
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"python": "Python 3.14.0"
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}
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-10-29T11:00:16.801535"
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}
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}

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