From b8f4e5fe34ae43edf52eb1713e206012d8751505 Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Fri, 1 May 2026 12:26:32 -0400 Subject: [PATCH 1/2] Adds stub block to gamma_gamma --- modules/nf-core/gamma/gamma/main.nf | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 5dad52498eee..21e54606296e 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -44,9 +44,14 @@ process GAMMA_GAMMA { $db \\ $prefix fi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gamma: $VERSION - END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.gamma + touch ${prefix}.psl + touch ${prefix}.gff + touch ${prefix}.fasta """ } From 5759411031b73cde3f10c25e2610e7bbc22248b1 Mon Sep 17 00:00:00 2001 From: Marcel Ribeiro-Dantas Date: Fri, 1 May 2026 12:26:57 -0400 Subject: [PATCH 2/2] Update gamma/gamma to using the versions topic channel --- modules/nf-core/gamma/gamma/main.nf | 12 ++--- modules/nf-core/gamma/gamma/meta.yml | 26 ++++++++--- .../gamma/gamma/tests/main.nf.test.snap | 44 +++++++++++++------ 3 files changed, 56 insertions(+), 26 deletions(-) diff --git a/modules/nf-core/gamma/gamma/main.nf b/modules/nf-core/gamma/gamma/main.nf index 21e54606296e..49d0b5d185a8 100644 --- a/modules/nf-core/gamma/gamma/main.nf +++ b/modules/nf-core/gamma/gamma/main.nf @@ -14,11 +14,12 @@ process GAMMA_GAMMA { path(db) output: - tuple val(meta), path("*.gamma") , emit: gamma - tuple val(meta), path("*.psl") , emit: psl - tuple val(meta), path("*.gff") , optional:true , emit: gff - tuple val(meta), path("*.fasta"), optional:true , emit: fasta - path "versions.yml" , emit: versions + tuple val(meta), path("*.gamma") , emit: gamma + tuple val(meta), path("*.psl") , emit: psl + tuple val(meta), path("*.gff") , optional:true , emit: gff + tuple val(meta), path("*.fasta"), optional:true , emit: fasta + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + tuple val("${task.process}"), val('gamma'), val("2.1"), emit: versions_gamma, topic: versions when: task.ext.when == null || task.ext.when @@ -26,7 +27,6 @@ process GAMMA_GAMMA { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ if [[ ${fasta} == *.gz ]] then diff --git a/modules/nf-core/gamma/gamma/meta.yml b/modules/nf-core/gamma/gamma/meta.yml index cff0025fc74c..62d699bf081d 100644 --- a/modules/nf-core/gamma/gamma/meta.yml +++ b/modules/nf-core/gamma/gamma/meta.yml @@ -75,13 +75,27 @@ output: description: multifasta file of the gene matches pattern: "*.{fasta}" ontologies: [] + versions_gamma: + - - ${task.process}: + type: string + description: The name of the process + - gamma: + type: string + description: The name of the tool + - "2.1": + type: string + description: The hard-coded 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 + - gamma: + type: string + description: The name of the tool + - "2.1": + type: string + description: The hard-coded version of the tool authors: - "@sateeshperi" - "@rastanton" diff --git a/modules/nf-core/gamma/gamma/tests/main.nf.test.snap b/modules/nf-core/gamma/gamma/tests/main.nf.test.snap index 19aa56e776a7..6dc46d02a8ae 100644 --- a/modules/nf-core/gamma/gamma/tests/main.nf.test.snap +++ b/modules/nf-core/gamma/gamma/tests/main.nf.test.snap @@ -33,7 +33,11 @@ ] ], "4": [ - "versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7" + [ + "GAMMA_GAMMA", + "gamma", + "2.1" + ] ], "fasta": [ [ @@ -65,16 +69,20 @@ "test.psl:md5,f489ce4602ddbcb692d5781ee3fbf449" ] ], - "versions": [ - "versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7" + "versions_gamma": [ + [ + "GAMMA_GAMMA", + "gamma", + "2.1" + ] ] } ], + "timestamp": "2026-05-01T12:25:09.793968", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-28T13:46:17.70616" + "nf-test": "0.9.4", + "nextflow": "26.04.0" + } }, "test-gamma": { "content": [ @@ -110,7 +118,11 @@ ] ], "4": [ - "versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7" + [ + "GAMMA_GAMMA", + "gamma", + "2.1" + ] ], "fasta": [ [ @@ -142,15 +154,19 @@ "test.psl:md5,162a2757ed3b167ae1e0cdb24213f940" ] ], - "versions": [ - "versions.yml:md5,cb429c7c459f700b16278ee01b8c46c7" + "versions_gamma": [ + [ + "GAMMA_GAMMA", + "gamma", + "2.1" + ] ] } ], + "timestamp": "2026-05-01T12:25:13.827116", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-28T13:46:24.433086" + "nf-test": "0.9.4", + "nextflow": "26.04.0" + } } } \ No newline at end of file