diff --git a/modules/nf-core/flumut/run/environment.yml b/modules/nf-core/flumut/run/environment.yml new file mode 100644 index 00000000000..22c826ae426 --- /dev/null +++ b/modules/nf-core/flumut/run/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::flumut=0.6.5" diff --git a/modules/nf-core/flumut/run/main.nf b/modules/nf-core/flumut/run/main.nf new file mode 100644 index 00000000000..e7699b7c780 --- /dev/null +++ b/modules/nf-core/flumut/run/main.nf @@ -0,0 +1,45 @@ +process FLUMUT_RUN { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "quay.io/biocontainers/flumut:0.6.5--pyhdfd78af_0" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + tuple val(meta), path("*.xlsm"), emit: xlsm + + tuple val("${task.process}"), val('flumut'), eval("flumut --all-versions"), topic: versions, emit: versions_flumut + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + flumut \\ + ${args} \\ + -x ${prefix}.xlsm \\ + -m ${prefix}_markers.tsv \\ + -M ${prefix}_mutations.tsv \\ + -l ${prefix}_literature.tsv \\ + ${fasta} + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo ${args} + + touch \\ + ${prefix}.xlsm \\ + ${prefix}_markers.tsv \\ + ${prefix}_mutations.tsv \\ + ${prefix}_literature.tsv + """ +} diff --git a/modules/nf-core/flumut/run/meta.yml b/modules/nf-core/flumut/run/meta.yml new file mode 100644 index 00000000000..3c6a71eade9 --- /dev/null +++ b/modules/nf-core/flumut/run/meta.yml @@ -0,0 +1,85 @@ +name: "flumut_run" +description: Run the FluMut tool to search for molecular markers with potential + impact on the biological characteristics of Influenza A viruses of the A(H5N1) + subtype. +keywords: + - FluMut + - mutations + - surveillance + - H5N1 + - Avian Influenza Virus +tools: + - "flumut": + description: "A tool to search for molecular markers with potential impact on + the biological characteristics of Influenza A viruses of the A(H5N1) subtype." + homepage: "https://github.com/izsvenezie-virology/FluMut" + documentation: "https://izsvenezie-virology.github.io/FluMut/" + tool_dev_url: "https://github.com/izsvenezie-virology/FluMut" + doi: "10.1093/ve/veaf011" + licence: + - "AGPL v3-or-later" + identifier: biotools:flumut +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The FASTA containing al the sequences to be analyzed + pattern: "*.{fa,fasta,fas}" + ontologies: + - edam: "http://edamontology.org/format_1929" +output: + tsv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: TSV files containing results + pattern: "*.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" + xlsm: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.xlsm": + type: file + description: Excel file containing results + pattern: "*.{xlsm}" + ontologies: + - edam: "http://edamontology.org/format_3468" + versions_flumut: + - - ${task.process}: + type: string + description: The name of the process + - flumut: + type: string + description: The name of the tool + - flumut --all-versions: + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - flumut: + type: string + description: The name of the tool + - flumut --all-versions: + type: eval + description: The expression to obtain the version of the tool +authors: + - "@EdoardoGiussani" + - "@AlexSartori" +maintainers: + - "@EdoardoGiussani" + - "@AlexSartori" diff --git a/modules/nf-core/flumut/run/tests/main.nf.test b/modules/nf-core/flumut/run/tests/main.nf.test new file mode 100644 index 00000000000..14ed4f1aeee --- /dev/null +++ b/modules/nf-core/flumut/run/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process FLUMUT_RUN" + script "../main.nf" + process "FLUMUT_RUN" + + tag "modules" + tag "modules_nfcore" + tag "flumut" + tag "flumut/run" + + test("H5N1_2.3.4.4b_Italy - fasta") { + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/virus/influenza/fasta/H5N1_2.3.4.4b_Italy.fa', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.tsv, + file(process.out.xlsm[0][1]).name, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("H5N1_2.3.4.4b_Italy - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/virus/influenza/fasta/H5N1_2.3.4.4b_Italy.fa', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/flumut/run/tests/main.nf.test.snap b/modules/nf-core/flumut/run/tests/main.nf.test.snap new file mode 100644 index 00000000000..fc4ff94b61e --- /dev/null +++ b/modules/nf-core/flumut/run/tests/main.nf.test.snap @@ -0,0 +1,98 @@ +{ + "H5N1_2.3.4.4b_Italy - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test_literature.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_markers.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_mutations.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + "FLUMUT_RUN", + "flumut", + "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + [ + "test_literature.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_markers.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_mutations.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_flumut": [ + [ + "FLUMUT_RUN", + "flumut", + "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17" + ] + ], + "xlsm": [ + [ + { + "id": "test" + }, + "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-05-22T12:11:02.098163186", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.04.6" + } + }, + "H5N1_2.3.4.4b_Italy - fasta": { + "content": [ + [ + [ + { + "id": "test" + }, + [ + "test_literature.tsv:md5,8999b029cb5cfcde7a4281cbcb3285c9", + "test_markers.tsv:md5,cbdc33bff11829875d7a88c3bd8d0303", + "test_mutations.tsv:md5,5c2d23a12a8fe807c237d952753daf3a" + ] + ] + ], + "test.xlsm", + { + "versions_flumut": [ + [ + "FLUMUT_RUN", + "flumut", + "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17" + ] + ] + } + ], + "timestamp": "2026-05-22T12:10:54.114556478", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.04.6" + } + } +} \ No newline at end of file