From 4f9854884d7d59e2e3f32403a8732be72d1a882b Mon Sep 17 00:00:00 2001 From: MohineTAlam Date: Thu, 22 Jan 2026 16:51:34 +0000 Subject: [PATCH 1/6] updated versions --- modules/nf-core/miniasm/main.nf | 10 +---- modules/nf-core/miniasm/meta.yml | 28 +++++++++---- .../nf-core/miniasm/tests/main.nf.test.snap | 40 +++++++++++++------ 3 files changed, 50 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf index afb4c0e327bc..25296e91908d 100644 --- a/modules/nf-core/miniasm/main.nf +++ b/modules/nf-core/miniasm/main.nf @@ -13,7 +13,7 @@ process MINIASM { output: tuple val(meta), path("*.gfa.gz") , emit: gfa tuple val(meta), path("*.fasta.gz"), emit: assembly - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('miniasm'), eval('miniasm -V 2>&1'), emit: versions_miniasm, topic: versions when: task.ext.when == null || task.ext.when @@ -33,10 +33,6 @@ process MINIASM { gzip -n ${prefix}.gfa gzip -n ${prefix}.fasta - cat <<-END_VERSIONS > versions.yml - "${task.process}": - miniasm: \$( miniasm -V 2>&1 ) - END_VERSIONS """ stub: @@ -45,10 +41,6 @@ process MINIASM { echo "" | gzip > ${prefix}.gfa.gz echo "" | gzip > ${prefix}.fasta.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - miniasm: \$( miniasm -V 2>&1 ) - END_VERSIONS """ } diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 52fea6d77b96..e7bd6bf52ca8 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -56,13 +56,27 @@ output: pattern: "*.fasta.gz" ontologies: - edam: http://edamontology.org/format_3989 # GZIP format - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_miniasm: + - - "${task.process}": + type: string + description: The name of the process + - miniasm: + type: string + description: The name of the tool + - miniasm -V 2>&1: + type: eval + description: The expression to obtain the version of the tool +topics: + versions_miniasm: + - - "${task.process}": + type: string + description: The name of the process + - miniasm: + type: string + description: The name of the tool + - miniasm -V 2>&1: + type: eval + description: The expression to obtain the version of the tool authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/miniasm/tests/main.nf.test.snap b/modules/nf-core/miniasm/tests/main.nf.test.snap index 005c425ddaa5..fb066c692da1 100644 --- a/modules/nf-core/miniasm/tests/main.nf.test.snap +++ b/modules/nf-core/miniasm/tests/main.nf.test.snap @@ -21,7 +21,11 @@ ] ], "2": [ - "versions.yml:md5,0572fb9059c7518d698bc5d609d63935" + [ + "MINIASM", + "miniasm", + "0.3-r179" + ] ], "assembly": [ [ @@ -41,16 +45,20 @@ "test.gfa.gz:md5,60e8b0c635905d20bc5296710749abde" ] ], - "versions": [ - "versions.yml:md5,0572fb9059c7518d698bc5d609d63935" + "versions_miniasm": [ + [ + "MINIASM", + "miniasm", + "0.3-r179" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-13T11:09:05.048611538" + "timestamp": "2026-01-22T16:50:51.951168082" }, "bacteroides_fragilis - [fastq.gz, paf]- fasta - stub": { "content": [ @@ -74,7 +82,11 @@ ] ], "2": [ - "versions.yml:md5,0572fb9059c7518d698bc5d609d63935" + [ + "MINIASM", + "miniasm", + "0.3-r179" + ] ], "assembly": [ [ @@ -94,15 +106,19 @@ "test.gfa.gz:md5,60e8b0c635905d20bc5296710749abde" ] ], - "versions": [ - "versions.yml:md5,0572fb9059c7518d698bc5d609d63935" + "versions_miniasm": [ + [ + "MINIASM", + "miniasm", + "0.3-r179" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-13T11:09:16.769292018" + "timestamp": "2026-01-22T16:50:58.724404158" } } \ No newline at end of file From 0ac5188283b6a8b372d680a03a7ea978076f8a46 Mon Sep 17 00:00:00 2001 From: MohineTAlam Date: Fri, 23 Jan 2026 09:20:14 +0000 Subject: [PATCH 2/6] Update modules/nf-core/miniasm/meta.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/miniasm/meta.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index e7bd6bf52ca8..4a3475b16b7b 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -57,15 +57,15 @@ output: ontologies: - edam: http://edamontology.org/format_3989 # GZIP format versions_miniasm: - - - "${task.process}": - type: string - description: The name of the process - - miniasm: - type: string - description: The name of the tool - - miniasm -V 2>&1: - type: eval - description: The expression to obtain the version of the tool + - - "${task.process}": + type: string + description: The name of the process + - miniasm: + type: string + description: The name of the tool + - miniasm -V 2>&1: + type: eval + description: The expression to obtain the version of the tool topics: versions_miniasm: - - "${task.process}": From 980d85554b3dde32808e6999a0b8fee40207cf60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 23 Jan 2026 12:15:40 +0100 Subject: [PATCH 3/6] Apply suggestion from @mashehu --- modules/nf-core/miniasm/meta.yml | 34 ++++++++++++++++---------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 4a3475b16b7b..391625f8e3bc 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -57,26 +57,26 @@ output: ontologies: - edam: http://edamontology.org/format_3989 # GZIP format versions_miniasm: - - - "${task.process}": - type: string - description: The name of the process - - miniasm: - type: string - description: The name of the tool - - miniasm -V 2>&1: - type: eval - description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - miniasm -V 2>&1: + type: eval + description: The expression to obtain the version of the tool topics: versions_miniasm: - - "${task.process}": - type: string - description: The name of the process - - miniasm: - type: string - description: The name of the tool - - miniasm -V 2>&1: - type: eval - description: The expression to obtain the version of the tool + type: string + description: The name of the process + - miniasm: + type: string + description: The name of the tool + - miniasm -V 2>&1: + type: eval + description: The expression to obtain the version of the tool authors: - "@avantonder" maintainers: From db1f19506bf51f89b28ac1f164e43cbe947e7c7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 23 Jan 2026 12:34:09 +0100 Subject: [PATCH 4/6] Apply suggestion from @mashehu --- modules/nf-core/miniasm/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 391625f8e3bc..fe55371c3de6 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -67,7 +67,7 @@ output: type: eval description: The expression to obtain the version of the tool topics: - versions_miniasm: + versions - - "${task.process}": type: string description: The name of the process From efa52de5ec06da895ae63b9c17dbd5b0fca17a61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 23 Jan 2026 12:39:19 +0100 Subject: [PATCH 5/6] Apply suggestion from @mashehu --- modules/nf-core/miniasm/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index fe55371c3de6..8a9c0a973269 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -67,7 +67,7 @@ output: type: eval description: The expression to obtain the version of the tool topics: - versions + versions: - - "${task.process}": type: string description: The name of the process From c925c53b4d87550b562ff8b5c2a4b0b106a8184a Mon Sep 17 00:00:00 2001 From: eit-maxlcummins Date: Mon, 26 Jan 2026 10:56:23 +0000 Subject: [PATCH 6/6] Update meta.yml change fastqc to miniasm - leftover boilerplate --- modules/nf-core/miniasm/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 8a9c0a973269..54293b55b640 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -60,7 +60,7 @@ output: - - ${task.process}: type: string description: The process the versions were collected from - - fastqc: + - miniasm: type: string description: The tool name - miniasm -V 2>&1: