From 6bbe8126ee3a461c7c1c7c4252972dc6958637ff Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 25 Apr 2026 07:38:31 +0200 Subject: [PATCH 1/3] Make input taxonomy files properly compliant --- modules/nf-core/krakenuniq/build/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf index d491b1010bf4..b20af96c735a 100644 --- a/modules/nf-core/krakenuniq/build/main.nf +++ b/modules/nf-core/krakenuniq/build/main.nf @@ -8,7 +8,7 @@ process KRAKENUNIQ_BUILD { : 'quay.io/biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2'}" input: - tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy"), path(custom_seqid2taxid) + tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy/*"), path(custom_seqid2taxid, stageAs: 'seqid2taxid.map') val keep_intermediate output: From 25815949faaaada264e34ffc229d3e4247bfb262 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 25 Apr 2026 09:07:59 +0200 Subject: [PATCH 2/3] Update snapshot to include the taxonomy files --- .../krakenuniq/build/tests/main.nf.test.snap | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap index b4007b93ec73..28e20259c6f3 100644 --- a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap +++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap @@ -60,13 +60,25 @@ "library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717", "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6", "seqid2taxid.map:md5,fe738f2333d57dde0db32239c04a93b8", - "taxDB:md5,1accaa141403e1fd5be9c79d1e5872b4" + "taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c", + "citations.dmp:md5,7b2e5d0fbea3da110c4a0e3bb7c3720d", + "division.dmp:md5,f93fc4c838fdaa4b8923f003e8c11712", + "gc.prt:md5,accfbf13bca0899e7ba9849195af241a", + "gencode.dmp:md5,a5f39fc7a6608775d4c62a96cf1d170c", + "images.dmp:md5,3855c67cfa06ef8ae713cab73f009e3d", + "merged.dmp:md5,5e78eb1c4a235889458ef9f83a64e81e", + "readme.txt:md5,051060a90b7b89ad8e0fa33fe280211c" ], [ + "database-build.log", "database-build.log", "database.report.tsv", + "delnodes.dmp", + "names.dmp", "names.dmp", "nodes.dmp", + "nodes.dmp", + "taxdump.tar.gz", "taxdump.tar.gz", "timestamp" ], @@ -76,9 +88,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.10.4" }, - "timestamp": "2025-03-06T09:49:11.884850884" + "timestamp": "2026-04-25T08:41:08.664355334" }, "sarscov2 - fasta": { "content": [ @@ -87,7 +99,7 @@ "database.kdb:md5,46542be19979e867075f9e455a314e00", "database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3", "database0.kdb:md5,46542be19979e867075f9e455a314e00", - "taxDB:md5,1accaa141403e1fd5be9c79d1e5872b4" + "taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c" ], [ @@ -98,8 +110,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.10.4" }, - "timestamp": "2025-03-06T09:48:27.136442441" + "timestamp": "2026-04-25T08:40:14.729177896" } } \ No newline at end of file From 5112744e4414bd196677300120252eede4f1eb01 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 25 Apr 2026 14:06:25 +0200 Subject: [PATCH 3/3] Topics conversion for all krakenuniq modules for linting Co-authored-by: Copilot --- modules/nf-core/krakenuniq/build/main.nf | 12 +- modules/nf-core/krakenuniq/build/meta.yml | 37 +++-- .../krakenuniq/build/tests/main.nf.test | 4 +- .../krakenuniq/build/tests/main.nf.test.snap | 58 +++++--- modules/nf-core/krakenuniq/download/main.nf | 12 +- modules/nf-core/krakenuniq/download/meta.yml | 37 +++-- .../krakenuniq/download/tests/main.nf.test | 2 +- .../download/tests/main.nf.test.snap | 46 ++++-- .../krakenuniq/preloadedkrakenuniq/main.nf | 22 +-- .../krakenuniq/preloadedkrakenuniq/meta.yml | 45 ++++-- .../preloadedkrakenuniq/tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 140 ++++++++++++------ 12 files changed, 255 insertions(+), 174 deletions(-) diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf index b20af96c735a..7fe9120d1da7 100644 --- a/modules/nf-core/krakenuniq/build/main.nf +++ b/modules/nf-core/krakenuniq/build/main.nf @@ -13,7 +13,7 @@ process KRAKENUNIQ_BUILD { output: tuple val(meta), path("${prefix}/"), emit: db - path "versions.yml", emit: versions + tuple val("${task.process}"), val('krakenuniq'), eval("krakenuniq --version | sed '1!d;s/KrakenUniq version //'"), emit: versions_krakenuniq, topic: versions when: task.ext.when == null || task.ext.when @@ -33,11 +33,6 @@ process KRAKENUNIQ_BUILD { --db ${prefix} ${run_cleanup} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ stub: @@ -52,10 +47,5 @@ process KRAKENUNIQ_BUILD { touch ${prefix}/database.kdb.counts touch ${prefix}/database.kraken.tsv touch ${prefix}/database.report.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/krakenuniq/build/meta.yml b/modules/nf-core/krakenuniq/build/meta.yml index 7aacb8341ebb..7b17a5de1da6 100644 --- a/modules/nf-core/krakenuniq/build/meta.yml +++ b/modules/nf-core/krakenuniq/build/meta.yml @@ -14,7 +14,8 @@ tools: documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:KrakenUniq input: - - meta: @@ -24,12 +25,13 @@ input: e.g. [ id:'test', single_end:false ] - custom_library_dir: type: directory - description: Optional directory containing custom fasta files for database build + description: Optional directory containing custom fasta files for database + build pattern: "*" - custom_taxonomy_dir: type: directory - description: Optional directory containing custom taxonomy files for database - build + description: Optional directory containing custom taxonomy files for + database build pattern: "*" - custom_seqid2taxid: type: file @@ -39,7 +41,6 @@ input: type: boolean description: "Keep intermediate files that are not used by the database itself" pattern: true|false - output: db: - - meta: @@ -51,13 +52,27 @@ output: type: directory description: Directory containing KrakenUniq database pattern: "*/" + versions_krakenuniq: + - - ${task.process}: + type: string + description: The name of the process + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq 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 + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test index c4e77e298460..da55baf00ac4 100644 --- a/modules/nf-core/krakenuniq/build/tests/main.nf.test +++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test @@ -55,7 +55,7 @@ nextflow_process { { assert snapshot( stablefiles.sort(), unstablefiles.sort(), - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) @@ -96,7 +96,7 @@ test("sarscov2 - fasta - nocleanup") { { assert snapshot( stablefiles.sort(), unstablefiles.sort(), - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap index 28e20259c6f3..cf902f8a687b 100644 --- a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap +++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "1": [ - "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325" + [ + "KRAKENUNIQ_BUILD", + "krakenuniq", + "1.0.4" + ] ], "db": [ [ @@ -37,16 +41,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325" + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_BUILD", + "krakenuniq", + "1.0.4" + ] ] } ], + "timestamp": "2026-04-25T13:34:52.419463205", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-03-06T09:45:24.957949175" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "sarscov2 - fasta - nocleanup": { "content": [ @@ -82,15 +90,21 @@ "taxdump.tar.gz", "timestamp" ], - [ - "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_BUILD", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T13:34:38.850675715", "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-25T08:41:08.664355334" + } }, "sarscov2 - fasta": { "content": [ @@ -104,14 +118,20 @@ [ ], - [ - "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_BUILD", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T13:33:43.689590026", "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-25T08:40:14.729177896" + } } } \ No newline at end of file diff --git a/modules/nf-core/krakenuniq/download/main.nf b/modules/nf-core/krakenuniq/download/main.nf index d03ffe6bfd95..22f8324fb087 100644 --- a/modules/nf-core/krakenuniq/download/main.nf +++ b/modules/nf-core/krakenuniq/download/main.nf @@ -11,7 +11,7 @@ process KRAKENUNIQ_DOWNLOAD { output: path "${pattern}/", emit: output - path "versions.yml", emit: versions + tuple val("${task.process}"), val('krakenuniq'), eval("krakenuniq --version | sed '1!d;s/KrakenUniq version //'"), emit: versions_krakenuniq, topic: versions when: task.ext.when == null || task.ext.when @@ -24,20 +24,10 @@ process KRAKENUNIQ_DOWNLOAD { -o ${pattern}/ \\ ${pattern} \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ stub: """ mkdir ${pattern} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/krakenuniq/download/meta.yml b/modules/nf-core/krakenuniq/download/meta.yml index 3f43e9571783..13e628ed1e04 100644 --- a/modules/nf-core/krakenuniq/download/meta.yml +++ b/modules/nf-core/krakenuniq/download/meta.yml @@ -14,26 +14,41 @@ tools: documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:KrakenUniq input: - pattern: type: string - description: Pattern indicating what type of NCBI data to download. See KrakenUniq - documnation for possibilities. + description: Pattern indicating what type of NCBI data to download. See + KrakenUniq documnation for possibilities. output: output: - ${pattern}/: type: directory - description: Directory containing downloaded data with directory naming being - the user provided pattern. + description: Directory containing downloaded data with directory naming + being the user provided pattern. + versions_krakenuniq: + - - ${task.process}: + type: string + description: The name of the process + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq 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 + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/download/tests/main.nf.test b/modules/nf-core/krakenuniq/download/tests/main.nf.test index 61f018208db4..bb4ce37c4fc0 100644 --- a/modules/nf-core/krakenuniq/download/tests/main.nf.test +++ b/modules/nf-core/krakenuniq/download/tests/main.nf.test @@ -31,7 +31,7 @@ nextflow_process { { assert snapshot( stablefiles.sort(), unstablefiles.sort(), - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) diff --git a/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap index a73147027117..4676758367f7 100644 --- a/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap +++ b/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap @@ -8,42 +8,56 @@ ] ], "1": [ - "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09" + [ + "KRAKENUNIQ_DOWNLOAD", + "krakenuniq", + "1.0.4" + ] ], "output": [ [ ] ], - "versions": [ - "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09" + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_DOWNLOAD", + "krakenuniq", + "1.0.4" + ] ] } ], + "timestamp": "2026-04-25T13:55:19.581303023", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" - }, - "timestamp": "2025-01-17T08:39:20.362801897" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "taxonomy": { "content": [ [ - "names.dmp:md5,65ebde1f4f66a4fbdf306c6cb26a5d4b", - "nodes.dmp:md5,e3ef0e39b3d4122b3c698d753a338a7d" + "names.dmp:md5,f5c2d156c88cae0c1356db74150a515a", + "nodes.dmp:md5,fe5fbc46ca0209840d44fb90454313e5" ], [ "taxdump.tar.gz", "timestamp" ], - [ - "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_DOWNLOAD", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T13:55:13.288242079", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" - }, - "timestamp": "2025-01-17T10:35:20.487227167" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf index b1eb0766328f..e44eac3adbc1 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf @@ -21,7 +21,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ { tuple val(meta), path("*.unclassified.${sequence_type}.gz"), optional: true, emit: unclassified_reads tuple val(meta), path('*.krakenuniq.classified.txt'), optional: true, emit: classified_assignment tuple val(meta), path('*.krakenuniq.report.txt'), emit: report - path "versions.yml", emit: versions + tuple val("${task.process}"), val('krakenuniq'), eval("krakenuniq --version | sed '1!d;s/KrakenUniq version //'"), emit: versions_krakenuniq, topic: versions when: task.ext.when == null || task.ext.when @@ -71,11 +71,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ { done < ${command_inputs_file} ${compress_reads_command} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } else { @@ -105,11 +100,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ { done < ${command_inputs_file} ${compress_reads_command} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } @@ -170,11 +160,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ { done < ${command_inputs_file} echo "${compress_reads_command}" - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } else { @@ -217,11 +202,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ { done < ${command_inputs_file} echo "${compress_reads_command}" - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') - END_VERSIONS """ } } diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml index 06421657b9b0..35566a55f974 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml @@ -13,7 +13,8 @@ tools: homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:KrakenUniq input: - - meta: @@ -23,8 +24,8 @@ input: e.g. [ id:'test', single_end:false ] - sequences: type: file - description: List of input files containing sequences. All of them must be either - in FASTA or FASTQ format. + description: List of input files containing sequences. All of them must be + either in FASTA or FASTQ format. ontologies: [] - prefixes: type: string @@ -34,8 +35,8 @@ input: length to the 'sequences', or to the number of sequencing pairs. - sequence_type: type: string - description: Format of all given sequencing files as literal string, either 'fasta' - or 'fastq'. + description: Format of all given sequencing files as literal string, either + 'fasta' or 'fastq'. pattern: "{fasta,fastq}" - db: type: directory @@ -51,8 +52,8 @@ input: description: Whether to generate a report of relative abundances. - save_output: type: boolean - description: Whether to save a file reporting the taxonomic classification of - each input read. + description: Whether to save a file reporting the taxonomic classification + of each input read. output: classified_reads: - - meta: @@ -67,7 +68,7 @@ output: in the KrakenUniq reference database. pattern: "*.classified.{fastq,fasta}.gz" ontologies: - - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_1930 unclassified_reads: - - meta: type: map @@ -81,7 +82,7 @@ output: in the KrakenUniq reference database. pattern: "*.unclassified.{fastq,fasta}.gz" ontologies: - - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_1930 classified_assignment: - - meta: type: map @@ -108,13 +109,27 @@ output: and unclassified reads. pattern: "*.krakenuniq.report.txt" ontologies: [] + versions_krakenuniq: + - - ${task.process}: + type: string + description: The name of the process + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq 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 + - krakenuniq: + type: string + description: The name of the tool + - krakenuniq --version | sed '1!d;s/KrakenUniq version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@mjamy" - "@Midnighter" diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test index 30e149bc44ed..cdf869f9a387 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test @@ -59,7 +59,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fasta') }, ) } @@ -105,7 +105,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fasta_ramchunksize') }, ) } @@ -148,7 +148,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fastq-single') }, ) } @@ -193,7 +193,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fastq-paired') }, ) } @@ -238,7 +238,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fasta-stub') }, ) } @@ -283,7 +283,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fastq-single-stub') }, ) } @@ -330,7 +330,7 @@ nextflow_process { process.out.classified_reads, process.out.unclassified_reads, process.out.classified_assignment, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match('fastq-paired-stub') }, ) } diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap index b2b99fc4e320..67c61c5bda64 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap @@ -19,15 +19,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:18.785223561", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" - }, - "timestamp": "2025-05-13T08:43:33.760035467" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fastq-single-stub": { "content": [ @@ -67,15 +73,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:55.090683568", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T14:25:43.618168582" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fastq-single": { "content": [ @@ -97,15 +109,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:27.966381254", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T15:21:33.941412985" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fastq-paired": { "content": [ @@ -127,15 +145,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:37.743401481", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T15:21:43.622100223" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fasta-stub": { "content": [ @@ -175,15 +199,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:46.269034458", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T14:25:33.871634213" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fastq-paired-stub": { "content": [ @@ -223,15 +253,21 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:04:04.043234967", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T14:25:54.663232573" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, "fasta": { "content": [ @@ -253,14 +289,20 @@ ] ] ], - [ - "versions.yml:md5,6abf6c733f53fa3b6aaaa6f06864ef0c" - ] + { + "versions_krakenuniq": [ + [ + "KRAKENUNIQ_PRELOADEDKRAKENUNIQ", + "krakenuniq", + "1.0.4" + ] + ] + } ], + "timestamp": "2026-04-25T14:03:09.485857492", "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" - }, - "timestamp": "2024-10-30T14:45:02.199077563" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } } } \ No newline at end of file