From f91999a6bf9125b7e3a00585efc7796993b3464a Mon Sep 17 00:00:00 2001 From: Francisco Martin Garcia Date: Fri, 13 Mar 2026 09:50:09 -0300 Subject: [PATCH 1/2] Migrate annosine module to topic channels --- modules/nf-core/annosine/main.nf | 14 +------ modules/nf-core/annosine/meta.yml | 33 ++++++++++----- modules/nf-core/annosine/tests/main.nf.test | 2 +- .../nf-core/annosine/tests/main.nf.test.snap | 42 ++++++++++++------- 4 files changed, 53 insertions(+), 38 deletions(-) diff --git a/modules/nf-core/annosine/main.nf b/modules/nf-core/annosine/main.nf index fff02ae8eccb..ecb8205b3118 100644 --- a/modules/nf-core/annosine/main.nf +++ b/modules/nf-core/annosine/main.nf @@ -15,7 +15,7 @@ process ANNOSINE { output: tuple val(meta), path("${prefix}.log"), emit: log tuple val(meta), path("${prefix}.fa") , emit: fa, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('annosine'), eval('pip show annosine2 | grep "^Version" | sed "s/Version: //"'), emit: versions_annosine, topic: versions when: task.ext.when == null || task.ext.when @@ -23,7 +23,6 @@ process ANNOSINE { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}_annosine" - def VERSION = '2.0.8' // WARN: Manually update when changing Bioconda assets if ( "${fasta}" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ AnnoSINE_v2 \\ @@ -38,24 +37,13 @@ process ANNOSINE { ${prefix}/Seed_SINE.fa \\ ${prefix}.fa \\ || echo 'AnnoSINE_v2 did not find SINE sequences. See log for details!' - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - annosine: ${VERSION} - END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${meta.id}_annosine" - def VERSION = '2.0.8' // WARN: Manually update when changing Bioconda assets if ( "${fasta}" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.log touch ${prefix}.fa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - annosine: ${VERSION} - END_VERSIONS """ } diff --git a/modules/nf-core/annosine/meta.yml b/modules/nf-core/annosine/meta.yml index 4aa71240a370..3a0c82158eca 100644 --- a/modules/nf-core/annosine/meta.yml +++ b/modules/nf-core/annosine/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "annosine" description: Accelerating de novo SINE annotation in plant and animal genomes keywords: @@ -13,9 +12,9 @@ tools: documentation: "https://github.com/liaoherui/AnnoSINE_v2" tool_dev_url: "https://github.com/liaoherui/AnnoSINE_v2" doi: "10.1101/2024.03.01.582874" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:annosine - input: - - meta: type: map @@ -27,7 +26,7 @@ input: description: Input genome assembly pattern: "*.{fasta,fa,fsa}" ontologies: - - edam: http://edamontology.org/format_1929 # FASTA + - edam: http://edamontology.org/format_1929 - mode: type: integer description: | @@ -59,13 +58,27 @@ output: description: | Non-redundant SINE library with serial number pattern: "*.{fa}" + versions_annosine: + - - "${task.process}": + type: string + description: The name of the process + - "annosine": + type: string + description: The name of the tool + - 'pip show annosine2 | grep "^Version" | sed "s/Version: //"': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - "${task.process}": + type: string + description: The name of the process + - "annosine": + type: string + description: The name of the tool + - 'pip show annosine2 | grep "^Version" | sed "s/Version: //"': + type: eval + description: The expression to obtain the version of the tool authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/annosine/tests/main.nf.test b/modules/nf-core/annosine/tests/main.nf.test index 547d6be4d3b0..d83d6b668136 100644 --- a/modules/nf-core/annosine/tests/main.nf.test +++ b/modules/nf-core/annosine/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert path(process.out.log[0][1]).text.contains('AnnoSINE COMPLETE!') }, { assert snapshot( process.out.fa, - process.out.versions, + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) diff --git a/modules/nf-core/annosine/tests/main.nf.test.snap b/modules/nf-core/annosine/tests/main.nf.test.snap index fa8b44344756..0c63755354d1 100644 --- a/modules/nf-core/annosine/tests/main.nf.test.snap +++ b/modules/nf-core/annosine/tests/main.nf.test.snap @@ -10,15 +10,21 @@ "test_annosine.fa:md5,fc3bd39555133a1b50623bccc7d4cf9b" ] ], - [ - "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f" - ] + { + "versions_annosine": [ + [ + "ANNOSINE", + "annosine", + "2.0.8" + ] + ] + } ], + "timestamp": "2026-03-13T09:45:27.322794252", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-27T14:41:54.821745" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "actinidia_chinensis - fasta - stub": { "content": [ @@ -42,7 +48,11 @@ ] ], "2": [ - "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f" + [ + "ANNOSINE", + "annosine", + "2.0.8" + ] ], "fa": [ [ @@ -62,15 +72,19 @@ "test_annosine.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f" + "versions_annosine": [ + [ + "ANNOSINE", + "annosine", + "2.0.8" + ] ] } ], + "timestamp": "2026-03-13T09:46:04.662034254", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-03-27T14:40:02.826271" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From f6448ea7d803cdf30a0d4041d52c5790715e1bca Mon Sep 17 00:00:00 2001 From: Francisco Martin <30799842+garciafranciscomartn@users.noreply.github.com> Date: Fri, 13 Mar 2026 10:41:34 -0300 Subject: [PATCH 2/2] Add comment to FASTA ontology in meta.yml --- modules/nf-core/annosine/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/annosine/meta.yml b/modules/nf-core/annosine/meta.yml index 3a0c82158eca..9dec9b4a8671 100644 --- a/modules/nf-core/annosine/meta.yml +++ b/modules/nf-core/annosine/meta.yml @@ -26,7 +26,7 @@ input: description: Input genome assembly pattern: "*.{fasta,fa,fsa}" ontologies: - - edam: http://edamontology.org/format_1929 + - edam: http://edamontology.org/format_1929 #FASTA - mode: type: integer description: |