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markquintontullochmarkquintontulloch
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Merge branch 'ENSGENOMIO-18' into local_testing
2 parents 2eaa504 + ef8a3ea commit cc87db0

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‎.gitignore‎

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11
.nextflow*
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.nf-test*
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__pycache__/
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*.pyc
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.python-version

‎modules/ensembl/fasta/recombine/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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- ensembl-genomio=1.6.1

‎modules/ensembl/fasta/recombine/main.nf‎

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// See the NOTICE file distributed with this work for additional information
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// regarding copyright ownership.
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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// You may obtain a copy of the License at
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//
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// http://www.apache.org/licenses/LICENSE-2.0
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//
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// Unless required by applicable law or agreed to in writing, software
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// distributed under the License is distributed on an "AS IS" BASIS,
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// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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// See the License for the specific language governing permissions and
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// limitations under the License.
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process FASTA_RECOMBINE {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/ensembl-genomio:1.6.1--pyhdfd78af_0'
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: 'quay.io/biocontainers/ensembl-genomio:1.6.1--pyhdfd78af_0'}"
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input:
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tuple val(meta), path(fasta_manifest), path(agp)
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output:
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tuple val(meta), path("${meta.id}.fa"), emit: recombined_fasta
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tuple val("${task.process}"), val('fasta_recombine'), eval("fasta_recombine --version"), emit: versions_fasta_recombine, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = []
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if (params.chunk_id_regex) {
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def rx = params.chunk_id_regex.replace("'", "'\"'\"'")
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args << "--chunk-id-regex '${rx}'"
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}
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if (params.allow_revcomp) {
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args << "--allow-revcomp"
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}
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def has_agp = agp && agp.baseName != 'NO_FILE'
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if (has_agp) {
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args << "--agp-file ${agp}"
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}
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def out_fasta = "${meta.id}.fa"
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"""
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fasta_recombine \\
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--fasta-manifest ${fasta_manifest} \\
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--out-fasta ${out_fasta} \\
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${args.join(' ')}
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"""
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stub:
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"""
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out_fa="${meta.id}.fa"
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touch "\$out_fa"
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"""
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}

‎modules/ensembl/fasta/recombine/meta.yml‎

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name: "fasta_recombine"
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description: Recombine split FASTA sequences into a single FASTA file,
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optionally using an AGP file.
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keywords:
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- ensembl
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- fasta
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- genomics
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- genomio
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- recombine
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tools:
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- "fasta_recombine":
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description: "Recombine split FASTA sequences generated by ensembl-genomio."
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homepage: "https://github.com/Ensembl/ensembl-genomio"
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licence:
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- "Apache License version 2.0"
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identifier: ""
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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 meta information
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e.g. `[ id:'accession1' ]`
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- fasta_manifest:
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type: file
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description: Manifest file listing split FASTA files to recombine.
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pattern: "*.txt"
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ontologies: []
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- agp:
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type: file
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description:
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Optional AGP file describing how split sequence chunks should
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be recombined. Use NO_FILE when not required.
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pattern: "*.{agp,NO_FILE}"
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ontologies: []
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output:
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recombined_fasta:
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- - meta:
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type: map
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description: |
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Groovy Map containing meta information
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e.g. `[ id:'accession1' ]`
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- ${meta.id}.fa:
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type: file
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description: Recombined FASTA file.
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pattern: "*.fa"
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ontologies: []
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versions_fasta_recombine:
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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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- fasta_recombine:
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type: string
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description: The name of the tool.
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- ? fasta_recombine --version
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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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- fasta_recombine:
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type: string
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description: The name of the tool.
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- ? fasta_recombine --version
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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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- "ensembl-dev@ebi.ac.uk"
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maintainers:
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- "ensembl-dev@ebi.ac.uk"

‎modules/ensembl/fasta/recombine/tests/main.nf.test‎

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// See the NOTICE file distributed with this work for additional information
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// regarding copyright ownership.
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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// You may obtain a copy of the License at
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//
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// http://www.apache.org/licenses/LICENSE-2.0
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//
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// Unless required by applicable law or agreed to in writing, software
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// distributed under the License is distributed on an "AS IS" BASIS,
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// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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// See the License for the specific language governing permissions and
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// limitations under the License.
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// nf-core modules test fasta/recombine
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nextflow_process {
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name "Test Process FASTA_RECOMBINE"
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script "../main.nf"
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process "FASTA_RECOMBINE"
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tag "modules"
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tag "modules_ensembl"
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tag "fasta"
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tag "fasta/recombine"
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test("stub outputs: header mode") {
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when {
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options "-stub"
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process {
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"""
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def manifest = file("manifest.txt")
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manifest.text = "x\\n"
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def no_file = file("NO_FILE")
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no_file.text = ""
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input[0] = [
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[ id: 'test' ],
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manifest,
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no_file
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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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assert process.trace.tasks().size() == 1
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assert process.out.recombined_fasta.size() == 1
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assert process.success
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assert snapshot(process.out).match()
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}
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}
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test("stub outputs: AGP mode") {
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when {
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options "-stub"
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process {
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"""
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def manifest = file("manifest.txt")
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manifest.text = "x\\n"
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def agp = file("test.agp")
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agp.text = ""
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input[0] = [
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[ id: 'test' ],
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manifest,
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agp
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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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assert process.trace.tasks().size() == 1
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assert process.out.recombined_fasta.size() == 1
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assert process.success
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assert snapshot(process.out).match()
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}
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}
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}

‎modules/ensembl/fasta/recombine/tests/main.nf.test.snap‎

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{
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"stub outputs: AGP mode": {
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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.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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"FASTA_RECOMBINE",
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"fasta_recombine",
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"1.6.3"
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]
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],
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"recombined_fasta": [
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[
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{
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"id": "test"
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},
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"test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_fasta_recombine": [
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[
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"FASTA_RECOMBINE",
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"fasta_recombine",
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"1.6.3"
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]
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]
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}
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],
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"timestamp": "2026-05-14T14:39:11.350698",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.3"
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}
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},
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"stub outputs: header mode": {
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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.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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"FASTA_RECOMBINE",
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"fasta_recombine",
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"1.6.3"
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]
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],
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"recombined_fasta": [
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[
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{
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"id": "test"
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},
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"test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_fasta_recombine": [
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[
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"FASTA_RECOMBINE",
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"fasta_recombine",
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"1.6.3"
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]
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]
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}
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],
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"timestamp": "2026-05-14T14:39:09.216174",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.3"
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}
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}
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}

‎modules/ensembl/fasta/split/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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- ensembl-genomio=1.6.1

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