From a02aae19e9ce4bfd73a48a29aa2e4d164b698aec Mon Sep 17 00:00:00 2001 From: louis Date: Tue, 12 May 2026 19:04:57 +0200 Subject: [PATCH 1/6] Update to topics --- .../nf-core/hamronization/abricate/main.nf | 12 +--- .../nf-core/hamronization/abricate/meta.yml | 33 +++++++--- .../hamronization/abricate/tests/main.nf.test | 14 +++-- .../abricate/tests/main.nf.test.snap | 60 +++++++------------ 4 files changed, 55 insertions(+), 64 deletions(-) diff --git a/modules/nf-core/hamronization/abricate/main.nf b/modules/nf-core/hamronization/abricate/main.nf index 7198e655879d..922ae9f98549 100644 --- a/modules/nf-core/hamronization/abricate/main.nf +++ b/modules/nf-core/hamronization/abricate/main.nf @@ -16,7 +16,7 @@ process HAMRONIZATION_ABRICATE { output: tuple val(meta), path("*.json"), optional: true, emit: json tuple val(meta), path("*.tsv"), optional: true, emit: tsv - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -33,21 +33,11 @@ process HAMRONIZATION_ABRICATE { --analysis_software_version ${software_version} \\ --reference_database_version ${reference_db_version} \\ > ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ } diff --git a/modules/nf-core/hamronization/abricate/meta.yml b/modules/nf-core/hamronization/abricate/meta.yml index 3e880b9f3f84..3451dbbdc63b 100644 --- a/modules/nf-core/hamronization/abricate/meta.yml +++ b/modules/nf-core/hamronization/abricate/meta.yml @@ -1,6 +1,6 @@ name: "hamronization_abricate" -description: Tool to convert and summarize ABRicate outputs using the hAMRonization - specification +description: Tool to convert and summarize ABRicate outputs using the + hAMRonization specification keywords: - amr - antimicrobial resistance @@ -13,7 +13,8 @@ tools: homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - - meta: @@ -65,13 +66,27 @@ output: pattern: "*.json" ontologies: - edam: http://edamontology.org/format_3464 # JSON + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/hamronization/abricate/tests/main.nf.test b/modules/nf-core/hamronization/abricate/tests/main.nf.test index d6c213503513..4b94c0206fab 100644 --- a/modules/nf-core/hamronization/abricate/tests/main.nf.test +++ b/modules/nf-core/hamronization/abricate/tests/main.nf.test @@ -14,7 +14,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] + input[0] = [ + [ id:"test" ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) + ] input[1] = 'tsv' input[2] = '1.0.1' input[3] = '2021-Mar-27' @@ -25,7 +28,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -37,7 +40,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ] + input[0] = [ + [ id:"test" ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) + ] input[1] = 'tsv' input[2] = '1.0.1' input[3] = '2021-Mar-27' @@ -48,7 +54,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/hamronization/abricate/tests/main.nf.test.snap b/modules/nf-core/hamronization/abricate/tests/main.nf.test.snap index c4ee869bb1e6..9d0ba13e527d 100644 --- a/modules/nf-core/hamronization/abricate/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/abricate/tests/main.nf.test.snap @@ -2,20 +2,6 @@ "hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "test.tsv:md5,4b1024ba25c116a5312944f65dd40e9b" - ] - ], - "2": [ - "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff" - ], "json": [ ], @@ -27,34 +13,24 @@ "test.tsv:md5,4b1024ba25c116a5312944f65dd40e9b" ] ], - "versions": [ - "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff" + "versions_hamronization": [ + [ + "HAMRONIZATION_ABRICATE", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:02:34.937482681", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:44:38.664437882" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } }, "hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff" - ], "json": [ ], @@ -66,15 +42,19 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff" + "versions_hamronization": [ + [ + "HAMRONIZATION_ABRICATE", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:02:41.628540543", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:44:45.131612041" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } } } \ No newline at end of file From 87ab86726412aafbf441bd676b1829919b7984dc Mon Sep 17 00:00:00 2001 From: louis Date: Tue, 12 May 2026 19:24:11 +0200 Subject: [PATCH 2/6] Update meta --- .../nf-core/hamronization/abricate/meta.yml | 6 +-- .../hamronization/amrfinderplus/meta.yml | 41 ++++++++++++------ .../nf-core/hamronization/deeparg/meta.yml | 43 +++++++++++++------ .../nf-core/hamronization/fargene/meta.yml | 39 +++++++++++------ modules/nf-core/hamronization/rgi/meta.yml | 38 +++++++++++----- .../nf-core/hamronization/summarize/meta.yml | 40 +++++++++++------ 6 files changed, 142 insertions(+), 65 deletions(-) diff --git a/modules/nf-core/hamronization/abricate/meta.yml b/modules/nf-core/hamronization/abricate/meta.yml index 3451dbbdc63b..e793d73218ca 100644 --- a/modules/nf-core/hamronization/abricate/meta.yml +++ b/modules/nf-core/hamronization/abricate/meta.yml @@ -21,7 +21,7 @@ input: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - report: type: file description: Output TSV or CSV file from ABRicate @@ -47,7 +47,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.json": type: file description: hAMRonised report in JSON format @@ -59,7 +59,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.tsv": type: file description: hAMRonised report in TSV format diff --git a/modules/nf-core/hamronization/amrfinderplus/meta.yml b/modules/nf-core/hamronization/amrfinderplus/meta.yml index 5751803c1965..454ed61b93b8 100644 --- a/modules/nf-core/hamronization/amrfinderplus/meta.yml +++ b/modules/nf-core/hamronization/amrfinderplus/meta.yml @@ -1,6 +1,6 @@ name: "hamronization_amrfinderplus" -description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization - specification. +description: Tool to convert and summarize AMRfinderPlus outputs using the + hAMRonization specification. keywords: - amr - antimicrobial resistance @@ -15,20 +15,21 @@ tools: homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - report: type: file description: Output .tsv file from AMRfinderPlus pattern: "*.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 - format: type: string description: Type of report file to be produced @@ -47,7 +48,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.json": type: file description: hAMRonised report in JSON format @@ -59,20 +60,34 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.tsv": type: file description: hAMRonised report in TSV format pattern: "*.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/deeparg/meta.yml b/modules/nf-core/hamronization/deeparg/meta.yml index ac447deda3e4..c3cdc9b97c27 100644 --- a/modules/nf-core/hamronization/deeparg/meta.yml +++ b/modules/nf-core/hamronization/deeparg/meta.yml @@ -1,6 +1,6 @@ name: hamronization_deeparg -description: Tool to convert and summarize DeepARG outputs using the hAMRonization - specification +description: Tool to convert and summarize DeepARG outputs using the + hAMRonization specification keywords: - amr - antimicrobial resistance @@ -8,19 +8,20 @@ keywords: - deeparg tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the - hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using + the hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - report: type: file description: Output .mapping.ARG file from DeepARG @@ -44,7 +45,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.json": type: file description: hAMRonised report in JSON format @@ -56,20 +57,34 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.tsv": type: file description: hAMRonised report in TSV format pattern: "*.json" ontologies: - edam: http://edamontology.org/format_3464 # JSON + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/fargene/meta.yml b/modules/nf-core/hamronization/fargene/meta.yml index addf6dce53f7..95342d32d90e 100644 --- a/modules/nf-core/hamronization/fargene/meta.yml +++ b/modules/nf-core/hamronization/fargene/meta.yml @@ -1,6 +1,6 @@ name: "hamronization_fargene" -description: Tool to convert and summarize fARGene outputs using the hAMRonization - specification +description: Tool to convert and summarize fARGene outputs using the + hAMRonization specification keywords: - amr - antimicrobial resistance @@ -15,14 +15,15 @@ tools: homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - report: type: file description: Output .txt file from fARGene @@ -46,7 +47,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.json": type: file description: hAMRonised report in JSON format @@ -58,20 +59,34 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.tsv": type: file description: hAMRonised report in TSV format pattern: "*.json" ontologies: - edam: http://edamontology.org/format_3464 # JSON + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/rgi/meta.yml b/modules/nf-core/hamronization/rgi/meta.yml index 3c83c293e818..ee2da0684949 100644 --- a/modules/nf-core/hamronization/rgi/meta.yml +++ b/modules/nf-core/hamronization/rgi/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_rgi" -description: Tool to convert and summarize RGI outputs using the hAMRonization specification. +description: Tool to convert and summarize RGI outputs using the hAMRonization + specification. keywords: - amr - antimicrobial resistance @@ -14,14 +15,15 @@ tools: homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - report: type: file description: Output .txt file from RGI @@ -45,7 +47,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.json": type: file description: hAMRonised report in JSON format @@ -57,20 +59,34 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.tsv": type: file description: hAMRonised report in TSV format pattern: "*.json" ontologies: - edam: http://edamontology.org/format_3464 # JSON + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/summarize/meta.yml b/modules/nf-core/hamronization/summarize/meta.yml index a37aa0475482..4970cc4f3d4b 100644 --- a/modules/nf-core/hamronization/summarize/meta.yml +++ b/modules/nf-core/hamronization/summarize/meta.yml @@ -1,23 +1,25 @@ name: hamronization_summarize -description: Tool to summarize and combine all hAMRonization reports into a single - file +description: Tool to summarize and combine all hAMRonization reports into a + single file keywords: - amr - antimicrobial resistance - reporting tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the - hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using + the hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization - licence: ["GNU Lesser General Public v3 (LGPL v3)"] + licence: + - "GNU Lesser General Public v3 (LGPL v3)" identifier: biotools:hamronization input: - reports: type: file - description: List of multiple hAMRonization reports in either JSON or TSV format + description: List of multiple hAMRonization reports in either JSON or TSV + format pattern: "*.{json,tsv}" ontologies: - edam: http://edamontology.org/format_3464 # JSON @@ -47,13 +49,27 @@ output: description: hAMRonised summary in HTML format pattern: "*.html" ontologies: [] + versions_hamronization: + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + 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 + - - ${task.process}: + type: string + description: The name of the process + - hamronization: + type: string + description: The name of the tool + - hamronize --version 2>&1 | sed 's/hamronize //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: From a241ab538ccc2b2dd233e1ccbb2a36c164f2d65e Mon Sep 17 00:00:00 2001 From: louis Date: Tue, 12 May 2026 19:24:37 +0200 Subject: [PATCH 3/6] Update to topics --- .../hamronization/amrfinderplus/main.nf | 12 +--- .../amrfinderplus/tests/main.nf.test | 12 ++-- .../amrfinderplus/tests/main.nf.test.snap | 68 ++++++------------- 3 files changed, 28 insertions(+), 64 deletions(-) diff --git a/modules/nf-core/hamronization/amrfinderplus/main.nf b/modules/nf-core/hamronization/amrfinderplus/main.nf index 8a57f017dbbd..67645ea849fe 100644 --- a/modules/nf-core/hamronization/amrfinderplus/main.nf +++ b/modules/nf-core/hamronization/amrfinderplus/main.nf @@ -16,7 +16,7 @@ process HAMRONIZATION_AMRFINDERPLUS { output: tuple val(meta), path("*.json"), optional: true, emit: json tuple val(meta), path("*.tsv"), optional: true, emit: tsv - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -34,21 +34,11 @@ process HAMRONIZATION_AMRFINDERPLUS { --reference_database_version ${reference_db_version} \\ --input_file_name ${prefix} \\ > ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ } diff --git a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test index 8d1165a408b9..6ec8db53dcd9 100644 --- a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test +++ b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output_prot.tsv", checkIfExists: true) + [ id:'test' ], + file(params.modules_testdata_base_path + 'delete_me/amrfinderplus/test_output_prot.tsv', checkIfExists: true) ] input[1] = 'tsv' input[2] = '4.0.23' @@ -28,10 +28,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("hamronization/amrfinderplus - delete_me/amrfinderplus - tsv - stub") { @@ -42,7 +41,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map + [ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output_prot.tsv", checkIfExists: true) ] input[1] = 'tsv' @@ -55,10 +54,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test.snap b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test.snap index 8f01b9f23310..6f12788e17ea 100644 --- a/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test.snap @@ -2,83 +2,59 @@ "hamronization/amrfinderplus - delete_me/amrfinderplus - tsv - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,bb043ef684cba407b418320169e43fca" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,bb043ef684cba407b418320169e43fca" + "versions_hamronization": [ + [ + "HAMRONIZATION_AMRFINDERPLUS", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:12:08.572831029", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:44:58.153879797" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } }, "hamronization/amrfinderplus - delete_me/amrfinderplus - tsv": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,129da2f25d4d68ab106990f1ae31d999" - ] - ], - "2": [ - "versions.yml:md5,bb043ef684cba407b418320169e43fca" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,129da2f25d4d68ab106990f1ae31d999" ] ], - "versions": [ - "versions.yml:md5,bb043ef684cba407b418320169e43fca" + "versions_hamronization": [ + [ + "HAMRONIZATION_AMRFINDERPLUS", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:12:01.310459409", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T07:43:32.220753935" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } } } \ No newline at end of file From 2396e4d9527e5282abfed461beabe63b2ab31226 Mon Sep 17 00:00:00 2001 From: louis Date: Tue, 12 May 2026 19:24:58 +0200 Subject: [PATCH 4/6] Update to topics --- modules/nf-core/hamronization/deeparg/main.nf | 13 +--- .../hamronization/deeparg/tests/main.nf.test | 12 ++-- .../deeparg/tests/main.nf.test.snap | 68 ++++++------------- 3 files changed, 29 insertions(+), 64 deletions(-) diff --git a/modules/nf-core/hamronization/deeparg/main.nf b/modules/nf-core/hamronization/deeparg/main.nf index 25f83ff5803a..68002e2052a3 100644 --- a/modules/nf-core/hamronization/deeparg/main.nf +++ b/modules/nf-core/hamronization/deeparg/main.nf @@ -16,7 +16,7 @@ process HAMRONIZATION_DEEPARG { output: tuple val(meta), path("*.json"), optional: true, emit: json tuple val(meta), path("*.tsv"), optional: true, emit: tsv - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -34,22 +34,11 @@ process HAMRONIZATION_DEEPARG { --reference_database_version ${reference_db_version} \\ --input_file_name ${prefix} \\ > ${prefix}.${format} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ } diff --git a/modules/nf-core/hamronization/deeparg/tests/main.nf.test b/modules/nf-core/hamronization/deeparg/tests/main.nf.test index 91ae43bf1a9e..1e1d976f80df 100644 --- a/modules/nf-core/hamronization/deeparg/tests/main.nf.test +++ b/modules/nf-core/hamronization/deeparg/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2' @@ -28,7 +28,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } @@ -42,8 +42,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' input[2] = '1.0.2' @@ -55,7 +55,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/hamronization/deeparg/tests/main.nf.test.snap b/modules/nf-core/hamronization/deeparg/tests/main.nf.test.snap index 4fba8246b13e..0b0d9408b0c7 100644 --- a/modules/nf-core/hamronization/deeparg/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/deeparg/tests/main.nf.test.snap @@ -2,83 +2,59 @@ "hamronization/deeparg - bacteroides_fragilis - genome_mapping_potential_arg - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e574e91477c7753e96c2e8411419cec1" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e574e91477c7753e96c2e8411419cec1" + "versions_hamronization": [ + [ + "HAMRONIZATION_DEEPARG", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:12:39.885357769", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:45:13.092217921" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } }, "hamronization/deeparg - bacteroides_fragilis - genome_mapping_potential_arg": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,e886d665bf9fc266be8193859863d2f4" - ] - ], - "2": [ - "versions.yml:md5,e574e91477c7753e96c2e8411419cec1" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,e886d665bf9fc266be8193859863d2f4" ] ], - "versions": [ - "versions.yml:md5,e574e91477c7753e96c2e8411419cec1" + "versions_hamronization": [ + [ + "HAMRONIZATION_DEEPARG", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T19:12:32.178181915", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:45:06.201275925" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } } } \ No newline at end of file From 4fbf5cdb097d0d6913110d2b8dc796b20b146ddc Mon Sep 17 00:00:00 2001 From: louis Date: Tue, 12 May 2026 19:25:44 +0200 Subject: [PATCH 5/6] Update to topics --- modules/nf-core/hamronization/fargene/main.nf | 14 ++--------- .../hamronization/fargene/tests/main.nf.test | 13 +++++----- .../fargene/tests/main.nf.test.snap | 18 ++++++-------- modules/nf-core/hamronization/rgi/main.nf | 12 +--------- .../hamronization/rgi/tests/main.nf.test | 24 +++++++++---------- .../nf-core/hamronization/summarize/main.nf | 12 +--------- .../summarize/tests/main.nf.test | 12 ++++------ 7 files changed, 34 insertions(+), 71 deletions(-) diff --git a/modules/nf-core/hamronization/fargene/main.nf b/modules/nf-core/hamronization/fargene/main.nf index 935689f88f50..b3df0f7a82d2 100644 --- a/modules/nf-core/hamronization/fargene/main.nf +++ b/modules/nf-core/hamronization/fargene/main.nf @@ -16,7 +16,7 @@ process HAMRONIZATION_FARGENE { output: tuple val(meta), path("*.json"), optional: true, emit: json tuple val(meta), path("*.tsv"), optional: true, emit: tsv - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -34,21 +34,11 @@ process HAMRONIZATION_FARGENE { --reference_database_version ${reference_db_version} \\ --input_file_name ${prefix} \\ > ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - echo "stub" > ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS + touch ${prefix}.${format} """ } diff --git a/modules/nf-core/hamronization/fargene/tests/main.nf.test b/modules/nf-core/hamronization/fargene/tests/main.nf.test index a5c5f2f7dbe5..e13bc807c1e0 100644 --- a/modules/nf-core/hamronization/fargene/tests/main.nf.test +++ b/modules/nf-core/hamronization/fargene/tests/main.nf.test @@ -18,10 +18,10 @@ nextflow_process { script "../../../gunzip/main.nf" process { """ - input[0] = Channel.fromList([ - tuple([ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)) - ]) + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) + ] """ } } @@ -51,8 +51,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.tsv.get(0).get(1)).exists() }, // No md5 check because of empty file - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["tsv"])).match() } ) } } @@ -75,7 +74,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap b/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap index 253409d9d698..3c5a7fad9eaa 100644 --- a/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap @@ -1,15 +1,11 @@ { "versions": { - "content": [ - [ - "versions.yml:md5,47191a10b21a94d1bc74adc90004da28" - ] - ], + "content": null, + "timestamp": "2026-05-12T19:15:03.444047781", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:45:22.733458727" + "nf-test": "0.9.4", + "nextflow": "26.03.0" + } }, "hamronization/fargene - stub": { "content": [ @@ -44,10 +40,10 @@ ] } ], + "timestamp": "2025-10-04T06:45:29.001707963", "meta": { "nf-test": "0.9.2", "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:45:29.001707963" + } } } \ No newline at end of file diff --git a/modules/nf-core/hamronization/rgi/main.nf b/modules/nf-core/hamronization/rgi/main.nf index fd1d86c4ab3c..9934ff8667be 100644 --- a/modules/nf-core/hamronization/rgi/main.nf +++ b/modules/nf-core/hamronization/rgi/main.nf @@ -16,7 +16,7 @@ process HAMRONIZATION_RGI { output: tuple val(meta), path("*.json"), optional: true, emit: json tuple val(meta), path("*.tsv"), optional: true, emit: tsv - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -34,21 +34,11 @@ process HAMRONIZATION_RGI { --reference_database_version ${reference_db_version} \\ --input_file_name ${prefix} \\ > ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.${format} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ } diff --git a/modules/nf-core/hamronization/rgi/tests/main.nf.test b/modules/nf-core/hamronization/rgi/tests/main.nf.test index 4bf7b51b5459..5bdaffb9ef29 100644 --- a/modules/nf-core/hamronization/rgi/tests/main.nf.test +++ b/modules/nf-core/hamronization/rgi/tests/main.nf.test @@ -17,19 +17,19 @@ nextflow_process { run("UNTAR") { script "modules/nf-core/untar/main.nf" process { - """ - file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('data.tar.gz') + """ + file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('data.tar.gz') - input[0] = [ - [ ], - file("data.tar.gz") - ] - """ + input[0] = [ + [id: "test" ], + file('https://card.mcmaster.ca/latest/data', checkIfExists: true) + ] + """ } } run("RGI_CARDANNOTATION") { - script "modules/nf-core/rgi/cardannotation/main.nf" + script "../../../rgi/cardannotation/main.nf" process { """ input[0] = UNTAR.out.untar.map{ it[1] } @@ -38,11 +38,11 @@ nextflow_process { } run("RGI_MAIN") { - script "modules/nf-core/rgi/main/main.nf" + script "../../../rgi/main/main.nf" process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db @@ -68,7 +68,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -91,7 +91,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/hamronization/summarize/main.nf b/modules/nf-core/hamronization/summarize/main.nf index deff56398684..6d7c6f18f065 100644 --- a/modules/nf-core/hamronization/summarize/main.nf +++ b/modules/nf-core/hamronization/summarize/main.nf @@ -14,7 +14,7 @@ process HAMRONIZATION_SUMMARIZE { path ("hamronization_combined_report.json"), optional: true, emit: json path ("hamronization_combined_report.tsv"), optional: true, emit: tsv path ("hamronization_combined_report.html"), optional: true, emit: html - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization when: task.ext.when == null || task.ext.when @@ -29,21 +29,11 @@ process HAMRONIZATION_SUMMARIZE { -t ${format} \\ ${args} \\ -o hamronization_combined_report.${outformat} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ stub: def outformat = format == 'interactive' ? 'html' : format """ touch hamronization_combined_report.${outformat} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) - END_VERSIONS """ } diff --git a/modules/nf-core/hamronization/summarize/tests/main.nf.test b/modules/nf-core/hamronization/summarize/tests/main.nf.test index 4a1d40f0421c..b2f4eaff5133 100644 --- a/modules/nf-core/hamronization/summarize/tests/main.nf.test +++ b/modules/nf-core/hamronization/summarize/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test1', single_end:false ], // meta map + [ id:'test1' ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' @@ -31,7 +31,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test2', single_end:false ], // meta map + [ id:'test2' ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true), ] input[1] = 'tsv' @@ -52,9 +52,7 @@ nextflow_process { ch_deeparg_run_one .mix( ch_deeparg_run_two ) - .map{ - [ it[1] ] - } + .map{[ it[1] ]} .collect() .set { ch_input_for_summarize } @@ -67,7 +65,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -99,7 +97,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } From 9759c947c352e58ca3c6b426a054c8bf8dd24976 Mon Sep 17 00:00:00 2001 From: louislenezet Date: Tue, 12 May 2026 17:38:01 +0000 Subject: [PATCH 6/6] Update version --- .../fargene/tests/main.nf.test.snap | 53 +++++++++------ .../hamronization/rgi/tests/main.nf.test.snap | 68 ++++++------------- .../summarize/tests/main.nf.test.snap | 56 ++++++--------- 3 files changed, 74 insertions(+), 103 deletions(-) diff --git a/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap b/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap index 3c5a7fad9eaa..9a343a44fc41 100644 --- a/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/fargene/tests/main.nf.test.snap @@ -1,29 +1,36 @@ { - "versions": { - "content": null, - "timestamp": "2026-05-12T19:15:03.444047781", - "meta": { - "nf-test": "0.9.4", - "nextflow": "26.03.0" - } - }, - "hamronization/fargene - stub": { + "hamronization/fargene - bacteroides_fragilis - illumina - fa.gz/gunzip": { "content": [ { - "0": [ + "json": [ ], - "1": [ + "tsv": [ [ { "id": "test" }, - "test.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.tsv" ] ], - "2": [ - "versions.yml:md5,47191a10b21a94d1bc74adc90004da28" - ], + "versions_hamronization": [ + [ + "HAMRONIZATION_FARGENE", + "hamronization", + "1.1.9" + ] + ] + } + ], + "timestamp": "2026-05-12T17:31:25.066871265", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "hamronization/fargene - stub": { + "content": [ + { "json": [ ], @@ -32,18 +39,22 @@ { "id": "test" }, - "test.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,47191a10b21a94d1bc74adc90004da28" + "versions_hamronization": [ + [ + "HAMRONIZATION_FARGENE", + "hamronization", + "1.1.9" + ] ] } ], - "timestamp": "2025-10-04T06:45:29.001707963", + "timestamp": "2026-05-12T17:31:36.519338002", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/modules/nf-core/hamronization/rgi/tests/main.nf.test.snap b/modules/nf-core/hamronization/rgi/tests/main.nf.test.snap index 6f8584b4bb09..c07493220fb9 100644 --- a/modules/nf-core/hamronization/rgi/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/rgi/tests/main.nf.test.snap @@ -2,83 +2,59 @@ "hamronization/rgi - haemophilus_influenzae - genome - fna.gz - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,96088fe7e0384b18ee942d0f128b9b6f" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,96088fe7e0384b18ee942d0f128b9b6f" + "versions_hamronization": [ + [ + "HAMRONIZATION_RGI", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T17:37:03.564588123", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:46:45.119618673" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "hamronization/rgi - haemophilus_influenzae - genome - fna.gz": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,fda542e7a38cb5c36d3c2912aebeae16" - ] - ], - "2": [ - "versions.yml:md5,96088fe7e0384b18ee942d0f128b9b6f" - ], "json": [ ], "tsv": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.tsv:md5,fda542e7a38cb5c36d3c2912aebeae16" ] ], - "versions": [ - "versions.yml:md5,96088fe7e0384b18ee942d0f128b9b6f" + "versions_hamronization": [ + [ + "HAMRONIZATION_RGI", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T17:36:23.428320453", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:46:22.942437126" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/nf-core/hamronization/summarize/tests/main.nf.test.snap b/modules/nf-core/hamronization/summarize/tests/main.nf.test.snap index 84e41f9b5f51..63d734dc0462 100644 --- a/modules/nf-core/hamronization/summarize/tests/main.nf.test.snap +++ b/modules/nf-core/hamronization/summarize/tests/main.nf.test.snap @@ -2,18 +2,6 @@ "hamronization/summarize - stub": { "content": [ { - "0": [ - "hamronization_combined_report.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,7795008976fd609121a33030de224a15" - ], "html": [ ], @@ -23,32 +11,24 @@ "tsv": [ ], - "versions": [ - "versions.yml:md5,7795008976fd609121a33030de224a15" + "versions_hamronization": [ + [ + "HAMRONIZATION_SUMMARIZE", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T17:37:35.04854389", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:47:09.077195126" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "hamronization/summarize - bacteroides_fragilis - hamronization - arg": { "content": [ { - "0": [ - "hamronization_combined_report.json:md5,b27855689f41a9a95ddcfbf6c02d3528" - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,7795008976fd609121a33030de224a15" - ], "html": [ ], @@ -58,15 +38,19 @@ "tsv": [ ], - "versions": [ - "versions.yml:md5,7795008976fd609121a33030de224a15" + "versions_hamronization": [ + [ + "HAMRONIZATION_SUMMARIZE", + "hamronization", + "1.1.9" + ] ] } ], + "timestamp": "2026-05-12T17:37:21.615477459", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-10-04T06:46:56.556328649" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file