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takiifujita-uicharles-plessyTakahiro Fujitaamirata051Lea Picard
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New macse refinealignment (#10586)
* nf-core template for macse/refinealignment * First commit by Takii * Modified for main.nf * Remove TODO comment about optional inputs support Removed outdated TODO comment regarding optional inputs. * update on nf.test * fixed meta.yml * update meta.yml and delete TODO statements * all TODO statements removed and meta updated * add fa format * Updated main nf test * fixed with lint * change expression of obtaining version * Lint and fixed meta.yml * fixed meta.yml * lint fixed it * Solved problem of last PR * Changed depends on comment * Corrected test data URL to nf-core/test-datasets * fixed lint problem * fixed to correct test URL * Corrected URL expression in main.nf.test * fixed lint problem --------- Co-authored-by: Charles Plessy <charles.plessy@oist.jp> Co-authored-by: Takahiro Fujita <takahiro-fujita@deigo-login1.oist.jp> Co-authored-by: Amirata Ghaffarian <amirata.gh.m.n@gmail.com> Co-authored-by: Lea Picard <lea-picard@deigo-login3.oist.jp> Co-authored-by: Patricia Carolina Muskus Veitia <patricia-muskus@deigo-login4.oist.jp> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Takahiro Fujita <takahiro-fujita@deigo-login2.oist.jp> Co-authored-by: Takahiro Fujita <takahiro-fujita@deigo-login4.oist.jp> Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> Co-authored-by: Takahiro Fujita <takahiro-fujita@deigo-login3.oist.jp>
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‎modules/nf-core/macse/refinealignment/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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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::macse=2.07"

‎modules/nf-core/macse/refinealignment/main.nf‎

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process MACSE_REFINEALIGNMENT {
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tag "${meta}"
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label 'process_low'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/macse:2.07--hdfd78af_0'
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: 'biocontainers/macse:2.07--hdfd78af_0'}"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*_NT.{fa,fas,fasta,aln}"), emit: nt
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tuple val(meta), path("*_AA.{fa,fas,fasta,aln}"), emit: aa
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tuple val("${task.process}"), val("macse"), eval("macse --version | sed -n 's/.*V\\([0-9]*\\.[0-9]*\\).*/\\1/p'"), topic: versions, emit: versions_macse
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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 ?: fasta.baseName
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"""
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sed '/^>/!s/[[:space:]]//g' ${fasta} > ${prefix}.clean.fasta
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macse -prog refineAlignment \\
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-align ${prefix}.clean.fasta \\
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${args}
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"""
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stub:
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def prefix = task.ext.prefix ?: fasta.baseName
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"""
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echo ${args}
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touch ${prefix}_NT.fas
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touch ${prefix}_AA.fas
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"""
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}

‎modules/nf-core/macse/refinealignment/meta.yml‎

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name: "macse_refinealignment"
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description: improves the input nucleotide alignment in a codon-aware manner
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keywords:
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- multiple sequence alignment
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- codon-aware
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- fasta
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tools:
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- "macse":
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description: "MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts
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and Stop Codons."
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homepage: https://www.agap-ge2pop.org/macse/
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documentation: https://www.agap-ge2pop.org/macse/macse-documentation/
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tool_dev_url: https://github.com/nf-core/masce
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doi: "10.1371/journal.pone.0022594"
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licence:
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- "CeCILL 2.1"
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identifier: biotools:macse
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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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- fasta:
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type: file
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description: Aligned sequences in FASTA format. May be gzipped or
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uncompressed.
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pattern: "*.{fa,fas,fasta,aln}"
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ontologies:
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- edam: http://edamontology.org/format_2554
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- edam: http://edamontology.org/format_1921
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- edam: http://edamontology.org/format_1984
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output:
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nt:
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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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- "*_NT.{fa,fas,fasta,aln}":
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type: file
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description: Aligned sequences in FASTA format. May be gzipped or
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uncompressed.
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pattern: "*_NT.{fa,fas,fasta,aln}"
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ontologies:
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- edam: http://edamontology.org/format_2554
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- edam: http://edamontology.org/format_1921
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- edam: http://edamontology.org/format_1984
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aa:
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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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- "*_AA.{fa,fas,fasta,aln}":
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type: file
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description: Aligned sequences in FASTA format. May be gzipped or
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uncompressed.
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pattern: "*_AA.{fa,fas,fasta,aln}"
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ontologies:
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- edam: http://edamontology.org/format_2554
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- edam: http://edamontology.org/format_1921
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- edam: http://edamontology.org/format_1984
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versions_macse:
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- - "${task.process}":
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type: string
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description: The name of the process
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- macse:
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type: string
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description: The name of the tool
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- "macse --version | sed -n 's/.*V\\([0-9]*\\.[0-9]*\\).*/\\1/p'":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - "${task.process}":
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type: string
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description: The name of the process
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- macse:
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type: string
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description: The name of the tool
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- "macse --version | sed -n 's/.*V\\([0-9]*\\.[0-9]*\\).*/\\1/p'":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@charles-plessy"
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- "@pmuskusv"
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- "@takiifujita-ui"
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- "@leapicard"
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maintainers:
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- "@leapicard"

‎modules/nf-core/macse/refinealignment/tests/main.nf.test‎

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// nf-core modules test macse/refinealignment
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nextflow_process {
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name "Test Process MACSE_REFINEALIGNMENT"
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script "../main.nf"
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process "MACSE_REFINEALIGNMENT"
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tag "modules"
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tag "modules_nfcore"
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tag "macse"
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tag "macse/refinealignment"
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test("Raphidioptera - fasta") {
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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.modules_testdata_base_path + 'genomics/eukaryotes/Raphidioptera/Raphidioptera_BOLD_COI_final_align_NT.aln', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot (
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process.out.aa,
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process.out.nt,
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match()}
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)
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}
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}
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test("Raphidioptera - fasta - 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(params.modules_testdata_base_path + 'genomics/eukaryotes/Raphidioptera/Raphidioptera_BOLD_COI_final_align_NT.aln', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot (
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process.out.aa,
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process.out.nt,
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match()}
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)
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}
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}
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}

‎modules/nf-core/macse/refinealignment/tests/main.nf.test.snap‎

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{
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"Raphidioptera - fasta": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"Raphidioptera_BOLD_COI_final_align_NT.clean_AA.fasta:md5,360a9975879ec3786ecd3519b06db0d7"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"Raphidioptera_BOLD_COI_final_align_NT.clean_NT.fasta:md5,8c967ce79c68e25e75969779a23c2dd0"
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]
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],
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{
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"versions_macse": [
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[
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"MACSE_REFINEALIGNMENT",
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"macse",
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"2.07"
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]
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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": "25.10.4"
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},
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"timestamp": "2026-03-19T15:41:21.463432407"
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},
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"Raphidioptera - fasta - stub": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"Raphidioptera_BOLD_COI_final_align_NT_AA.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"Raphidioptera_BOLD_COI_final_align_NT_NT.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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{
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"versions_macse": [
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[
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"MACSE_REFINEALIGNMENT",
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"macse",
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"2.07"
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]
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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": "25.10.4"
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},
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"timestamp": "2026-03-19T15:41:36.724574677"
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}
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}

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