From bade90660a2d4dc6f2941f1a479b0d1351fcbd9b Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Mon, 18 Mar 2024 18:46:37 -0600 Subject: [PATCH 01/13] first commit --- modules/nf-core/kraken2/build/environment.yml | 9 ++ modules/nf-core/kraken2/build/main.nf | 46 ++++++++++ modules/nf-core/kraken2/build/meta.yml | 44 +++++++++ .../nf-core/kraken2/build/tests/main.nf.test | 89 +++++++++++++++++++ .../kraken2/build/tests/nextflow.config | 9 ++ modules/nf-core/kraken2/build/tests/tags.yml | 4 + 6 files changed, 201 insertions(+) create mode 100644 modules/nf-core/kraken2/build/environment.yml create mode 100644 modules/nf-core/kraken2/build/main.nf create mode 100644 modules/nf-core/kraken2/build/meta.yml create mode 100644 modules/nf-core/kraken2/build/tests/main.nf.test create mode 100644 modules/nf-core/kraken2/build/tests/nextflow.config create mode 100644 modules/nf-core/kraken2/build/tests/tags.yml diff --git a/modules/nf-core/kraken2/build/environment.yml b/modules/nf-core/kraken2/build/environment.yml new file mode 100644 index 00000000000..fd573b81ece --- /dev/null +++ b/modules/nf-core/kraken2/build/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "kraken2_build" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::kraken2=2.1.3" diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf new file mode 100644 index 00000000000..6ef50b9ee27 --- /dev/null +++ b/modules/nf-core/kraken2/build/main.nf @@ -0,0 +1,46 @@ +process KRAKEN2_BUILD { + tag "$meta.id" + label 'process_medium' + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-f8c4015c836dd3ce5c118cfed97ec8259bab9e9d:2e0b144854b4a3d69b5df7a0340a60db846cc8bf-0': + 'biocontainers/mulled-v2-f8c4015c836dd3ce5c118cfed97ec8259bab9e9d:2e0b144854b4a3d69b5df7a0340a60db846cc8bf-0' }" + + input: + tuple val(meta), path(db) + + output: + tuple val(meta), path("$prefix"), emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + kraken2-build \\ + --build \\ + $args \\ + --threads $task.cpus \\ + --db ${db} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir "$prefix" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml new file mode 100644 index 00000000000..ee4b173c37b --- /dev/null +++ b/modules/nf-core/kraken2/build/meta.yml @@ -0,0 +1,44 @@ +name: "kraken2_build" +description: Builds Kraken2 database +keywords: + - metagenomics + - db + - classification + - build + - kraken2 +tools: + - kraken2: + description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + homepage: https://ccb.jhu.edu/software/kraken2/ + documentation: https://github.com/DerrickWood/kraken2/wiki/Manual + tool_dev_url: "https://github.com/DerrickWood/kraken2" + doi: 10.1186/s13059-019-1891-0 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - db: + type: directory + description: contains required files to build the database + pattern: "*/" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - db: + type: directory + description: contains the database that can be used to perform taxonomic classification + pattern: "*/" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@alxndrdiaz" +maintainers: + - "@alxndrdiaz" diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test new file mode 100644 index 00000000000..94bf8de6f48 --- /dev/null +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + + name "Test Process KRAKEN2_BUILD" + script "../main.nf" + process "KRAKEN2_BUILD" + config "./nextflow.config" + tag "kraken2" + tag "kraken2/build" + tag "kraken2/add" + tag "gunzip" + tag "modules" + tag "modules_nfcore" + + setup { + + run("GUNZIP") { + script "modules/nf-core/gunzip/main.nf" + process { + """ + input[0] = Channel.of([ + [], + file( + params.test_data['sarscov2']['metagenome']['prot_accession2taxid_gz'], + checkIfExists: true + ) + ]) + """ + } + } + + run("KRAKEN2_ADD") { + script "modules/nf-core/kraken2/add/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) + ] + ] + input[1] = file(params.test_data['sarscov2']['metagenome']['prot_names_dmp'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['metagenome']['prot_nodes_dmp'], checkIfExists: true) + input[3] = GUNZIP.out.gunzip.map{ it[1] } + """ + } + } + + } + + test("sarscov2 protein_db") { + + when { + process { + """ + input[0] = KRAKEN2_ADD.out.db + """ + } + } + + then { + assertAll( + { assert process.success } + ) + } + + } + + test("sarscov2 protein_db stub") { + + options "-stub" + + when { + process { + """ + input[0] = KRAKEN2_ADD.out.db + """ + } + } + + then { + assertAll( + { assert process.success } + ) + } + + } + +} diff --git a/modules/nf-core/kraken2/build/tests/nextflow.config b/modules/nf-core/kraken2/build/tests/nextflow.config new file mode 100644 index 00000000000..11ac39e45ba --- /dev/null +++ b/modules/nf-core/kraken2/build/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: KRAKEN2_BUILD { + ext.args = '--protein' + } + +} diff --git a/modules/nf-core/kraken2/build/tests/tags.yml b/modules/nf-core/kraken2/build/tests/tags.yml new file mode 100644 index 00000000000..4a5e61d30d1 --- /dev/null +++ b/modules/nf-core/kraken2/build/tests/tags.yml @@ -0,0 +1,4 @@ +kraken2/build: + - modules/nf-core/kraken2/build/** + - modules/nf-core/kraken2/add/** + - modules/nf-core/gunzip/** From 4c38491c0f9fe7002af95e2d56b59ea04ea73ff6 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Tue, 19 Mar 2024 08:04:30 -0600 Subject: [PATCH 02/13] use mkdir -p flag --- modules/nf-core/kraken2/build/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index 6ef50b9ee27..574ee1962ed 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -36,7 +36,7 @@ process KRAKEN2_BUILD { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir "$prefix" + mkdir -p "$prefix" cat <<-END_VERSIONS > versions.yml "${task.process}": From 22ca0180d22a8c78111cc4570567187fa13f20d6 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Tue, 19 Mar 2024 17:58:47 -0600 Subject: [PATCH 03/13] update assertions --- .../nf-core/kraken2/build/tests/main.nf.test | 11 ++++- .../kraken2/build/tests/main.nf.test.snap | 49 +++++++++++++++++++ 2 files changed, 58 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/kraken2/build/tests/main.nf.test.snap diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test index 94bf8de6f48..3e1f64ad5b4 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -60,7 +60,12 @@ nextflow_process { then { assertAll( - { assert process.success } + { assert process.success }, + { assert process.out.db.get(0).get(1) ==~ ".*/test" }, + { assert snapshot ( + path("${process.out.db[0][1]}/seqid2taxid.map") + ).match() + } ) } @@ -80,7 +85,9 @@ nextflow_process { then { assertAll( - { assert process.success } + { assert process.success }, + { assert snapshot (process.out).match() + } ) } diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test.snap b/modules/nf-core/kraken2/build/tests/main.nf.test.snap new file mode 100644 index 00000000000..7cbf974c6d7 --- /dev/null +++ b/modules/nf-core/kraken2/build/tests/main.nf.test.snap @@ -0,0 +1,49 @@ +{ + "sarscov2 protein_db": { + "content": [ + "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T17:49:10.727894" + }, + "sarscov2 protein_db stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "1": [ + "versions.yml:md5,df044948ec1fdb342a1d6fadde84b334" + ], + "db": [ + [ + { + "id": "test" + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,df044948ec1fdb342a1d6fadde84b334" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T17:41:57.715748" + } +} \ No newline at end of file From 525fd1ed1082b39ee79c068fa86fa65b4f64c19f Mon Sep 17 00:00:00 2001 From: Alexander Ramos Date: Tue, 19 Mar 2024 21:02:15 -0600 Subject: [PATCH 04/13] Update modules/nf-core/kraken2/build/main.nf Co-authored-by: James A. Fellows Yates --- modules/nf-core/kraken2/build/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index 574ee1962ed..6032552653a 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -23,7 +23,7 @@ process KRAKEN2_BUILD { kraken2-build \\ --build \\ $args \\ - --threads $task.cpus \\ + --threads ${task.cpus} \\ --db ${db} cat <<-END_VERSIONS > versions.yml From d68f9fadf9d7d2b27a7b4765bd5cb433b436afe8 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Wed, 20 Mar 2024 17:00:26 -0600 Subject: [PATCH 05/13] update dependencies --- modules/nf-core/kraken2/build/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/kraken2/build/environment.yml b/modules/nf-core/kraken2/build/environment.yml index fd573b81ece..822f48907f6 100644 --- a/modules/nf-core/kraken2/build/environment.yml +++ b/modules/nf-core/kraken2/build/environment.yml @@ -7,3 +7,4 @@ channels: - defaults dependencies: - "bioconda::kraken2=2.1.3" + - "coreutils=9.4" From a4bce9c1f3a066073ebfbe3cb29118ebbbf0e4c9 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Wed, 20 Mar 2024 17:03:30 -0600 Subject: [PATCH 06/13] add args_id --- modules/nf-core/kraken2/build/meta.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml index ee4b173c37b..3dac0684af3 100644 --- a/modules/nf-core/kraken2/build/meta.yml +++ b/modules/nf-core/kraken2/build/meta.yml @@ -14,6 +14,7 @@ tools: tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + args_id: "$args" input: - meta: type: map From ffbdef5f3d0840370f92cf96cd6c73ab675bac6c Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Wed, 20 Mar 2024 18:54:21 -0600 Subject: [PATCH 07/13] option for cleaning files --- modules/nf-core/kraken2/build/main.nf | 4 +++- modules/nf-core/kraken2/build/meta.yml | 3 +++ modules/nf-core/kraken2/build/tests/main.nf.test | 5 ++++- modules/nf-core/kraken2/build/tests/main.nf.test.snap | 5 +++-- 4 files changed, 13 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index 6032552653a..bc9003e7e44 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -8,6 +8,7 @@ process KRAKEN2_BUILD { input: tuple val(meta), path(db) + val cleaning output: tuple val(meta), path("$prefix"), emit: db @@ -19,13 +20,14 @@ process KRAKEN2_BUILD { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + runclean = cleaning ? "kraken2-build --clean --db ${db}" : "" """ kraken2-build \\ --build \\ $args \\ --threads ${task.cpus} \\ --db ${db} - + $runclean cat <<-END_VERSIONS > versions.yml "${task.process}": kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml index 3dac0684af3..50f6d19379c 100644 --- a/modules/nf-core/kraken2/build/meta.yml +++ b/modules/nf-core/kraken2/build/meta.yml @@ -25,6 +25,9 @@ input: type: directory description: contains required files to build the database pattern: "*/" + - cleaning: + type: boolean + description: activate or deactivate (true or false) cleaning of intermediate files output: - meta: type: map diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test index 3e1f64ad5b4..24e56445b09 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -54,6 +54,7 @@ nextflow_process { process { """ input[0] = KRAKEN2_ADD.out.db + input[1] = true """ } } @@ -63,7 +64,8 @@ nextflow_process { { assert process.success }, { assert process.out.db.get(0).get(1) ==~ ".*/test" }, { assert snapshot ( - path("${process.out.db[0][1]}/seqid2taxid.map") + path("${process.out.db[0][1]}/hash.k2d"), + path("${process.out.db[0][1]}/taxo.k2d") ).match() } ) @@ -79,6 +81,7 @@ nextflow_process { process { """ input[0] = KRAKEN2_ADD.out.db + input[1] = true """ } } diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test.snap b/modules/nf-core/kraken2/build/tests/main.nf.test.snap index 7cbf974c6d7..cae9944ab69 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test.snap +++ b/modules/nf-core/kraken2/build/tests/main.nf.test.snap @@ -1,13 +1,14 @@ { "sarscov2 protein_db": { "content": [ - "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e" + "hash.k2d:md5,e9984a5e98f87c0488cb5e7618d5bbe0", + "taxo.k2d:md5,29d65b1796e09191fd7bdcaa24130459" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-19T17:49:10.727894" + "timestamp": "2024-03-20T18:43:06.653895" }, "sarscov2 protein_db stub": { "content": [ From b475a2362489a6ada05bc5f2940f70b03184877c Mon Sep 17 00:00:00 2001 From: Alexander Ramos Date: Thu, 21 Mar 2024 09:36:52 -0600 Subject: [PATCH 08/13] Update modules/nf-core/kraken2/build/main.nf Co-authored-by: James A. Fellows Yates --- modules/nf-core/kraken2/build/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index bc9003e7e44..e052d087236 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -28,6 +28,7 @@ process KRAKEN2_BUILD { --threads ${task.cpus} \\ --db ${db} $runclean + cat <<-END_VERSIONS > versions.yml "${task.process}": kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') From 52f1e3b241406ff5d9ecb6be42b5410cf5748e02 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Thu, 21 Mar 2024 10:34:08 -0600 Subject: [PATCH 09/13] remove trailing whitespace --- modules/nf-core/kraken2/build/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index e052d087236..964df05682c 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -27,7 +27,7 @@ process KRAKEN2_BUILD { $args \\ --threads ${task.cpus} \\ --db ${db} - $runclean + $runclean cat <<-END_VERSIONS > versions.yml "${task.process}": From ce57507973ac3c484944f83b5f511473304b1d12 Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Thu, 21 Mar 2024 10:38:32 -0600 Subject: [PATCH 10/13] remove trailing whitespace --- modules/nf-core/kraken2/build/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index 964df05682c..bc9003e7e44 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -27,8 +27,7 @@ process KRAKEN2_BUILD { $args \\ --threads ${task.cpus} \\ --db ${db} - $runclean - + $runclean cat <<-END_VERSIONS > versions.yml "${task.process}": kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') From 22bf0167eba2ec680bcac31fac4d4c37fa54e47b Mon Sep 17 00:00:00 2001 From: alxndrdiaz Date: Thu, 21 Mar 2024 17:12:21 -0600 Subject: [PATCH 11/13] check prefix and database name --- modules/nf-core/kraken2/build/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf index bc9003e7e44..48cba54b45c 100644 --- a/modules/nf-core/kraken2/build/main.nf +++ b/modules/nf-core/kraken2/build/main.nf @@ -28,6 +28,9 @@ process KRAKEN2_BUILD { --threads ${task.cpus} \\ --db ${db} $runclean + if [[ \$(basename ${db}) != "${prefix}" ]]; then + mv ${db}/* ${prefix} + fi cat <<-END_VERSIONS > versions.yml "${task.process}": kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') From 96f73d22be597e256f3e80eb343da074371ef740 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 22 Mar 2024 07:46:20 +0000 Subject: [PATCH 12/13] Add slightly relaxed assrtions opts.k2d --- modules/nf-core/kraken2/build/tests/main.nf.test | 14 ++++++++------ .../nf-core/kraken2/build/tests/main.nf.test.snap | 6 ++++-- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test index 24e56445b09..ecdb155a6cc 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -10,9 +10,9 @@ nextflow_process { tag "gunzip" tag "modules" tag "modules_nfcore" - + setup { - + run("GUNZIP") { script "modules/nf-core/gunzip/main.nf" process { @@ -27,7 +27,7 @@ nextflow_process { """ } } - + run("KRAKEN2_ADD") { script "modules/nf-core/kraken2/add/main.nf" process { @@ -52,7 +52,7 @@ nextflow_process { when { process { - """ + """ input[0] = KRAKEN2_ADD.out.db input[1] = true """ @@ -65,7 +65,9 @@ nextflow_process { { assert process.out.db.get(0).get(1) ==~ ".*/test" }, { assert snapshot ( path("${process.out.db[0][1]}/hash.k2d"), - path("${process.out.db[0][1]}/taxo.k2d") + path("${process.out.db[0][1]}/taxo.k2d"), + path("${process.out.db[0][1]}/unmapped.txt"), + file("${process.out.db[0][1]}/opts.k2d").name ).match() } ) @@ -79,7 +81,7 @@ nextflow_process { when { process { - """ + """ input[0] = KRAKEN2_ADD.out.db input[1] = true """ diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test.snap b/modules/nf-core/kraken2/build/tests/main.nf.test.snap index cae9944ab69..21c7b3854a4 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test.snap +++ b/modules/nf-core/kraken2/build/tests/main.nf.test.snap @@ -2,13 +2,15 @@ "sarscov2 protein_db": { "content": [ "hash.k2d:md5,e9984a5e98f87c0488cb5e7618d5bbe0", - "taxo.k2d:md5,29d65b1796e09191fd7bdcaa24130459" + "taxo.k2d:md5,29d65b1796e09191fd7bdcaa24130459", + "unmapped.txt:md5,1c04243f50ce0e7769ad7dce51285c7d", + "opts.k2d" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-20T18:43:06.653895" + "timestamp": "2024-03-22T07:43:51.068822397" }, "sarscov2 protein_db stub": { "content": [ From 21346f334aafee8ea83b081b9c663f9ce72219b4 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 22 Mar 2024 08:13:27 +0000 Subject: [PATCH 13/13] Change unmapped as well due to occasional variation --- modules/nf-core/kraken2/build/tests/main.nf.test | 4 ++-- modules/nf-core/kraken2/build/tests/main.nf.test.snap | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test index ecdb155a6cc..9eec2ccee92 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test +++ b/modules/nf-core/kraken2/build/tests/main.nf.test @@ -66,8 +66,8 @@ nextflow_process { { assert snapshot ( path("${process.out.db[0][1]}/hash.k2d"), path("${process.out.db[0][1]}/taxo.k2d"), - path("${process.out.db[0][1]}/unmapped.txt"), - file("${process.out.db[0][1]}/opts.k2d").name + file("${process.out.db[0][1]}/opts.k2d").name, + file("${process.out.db[0][1]}/unmapped.txt").name ).match() } ) diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test.snap b/modules/nf-core/kraken2/build/tests/main.nf.test.snap index 21c7b3854a4..fb87c518830 100644 --- a/modules/nf-core/kraken2/build/tests/main.nf.test.snap +++ b/modules/nf-core/kraken2/build/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "hash.k2d:md5,e9984a5e98f87c0488cb5e7618d5bbe0", "taxo.k2d:md5,29d65b1796e09191fd7bdcaa24130459", - "unmapped.txt:md5,1c04243f50ce0e7769ad7dce51285c7d", - "opts.k2d" + "opts.k2d", + "unmapped.txt" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-22T07:43:51.068822397" + "timestamp": "2024-03-22T08:10:48.644001909" }, "sarscov2 protein_db stub": { "content": [