diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml index 18547591a2e..235ad03ad82 100644 --- a/modules/nf-core/mmseqs/cluster/environment.yml +++ b/modules/nf-core/mmseqs/cluster/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=15.6f452 + - bioconda::mmseqs2=16.747c6 diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf index 408e4275647..bad704cbbe2 100644 --- a/modules/nf-core/mmseqs/cluster/main.nf +++ b/modules/nf-core/mmseqs/cluster/main.nf @@ -4,8 +4,8 @@ process MMSEQS_CLUSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': + 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" input: tuple val(meta), path(db_input) diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test b/modules/nf-core/mmseqs/cluster/tests/main.nf.test new file mode 100644 index 00000000000..07882216e3b --- /dev/null +++ b/modules/nf-core/mmseqs/cluster/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process MMSEQS_CLUSTER" + script "../main.nf" + process "MMSEQS_CLUSTER" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "mmseqs" + tag "mmseqs/cluster" + tag "untar" + + test("Should cluster an mmseqs database") { + + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/mmseqs.tar.gz', checkIfExists: true) ] + """ + } + } + } + + when { + process { + """ + input[0] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.db_cluster.size() == 1 }, + { + def all_files = file(process.out.db_cluster[0][1]).listFiles() + def all_file_names = all_files.collect { it.name }.toSorted() + def stable_file_names = [ + 'test_output_cluster.dbtype', + 'test_output_cluster.index' + ] + def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted() + + assert snapshot( + all_file_names, + stable_files, + process.out.versions[0] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap new file mode 100644 index 00000000000..6fc98698513 --- /dev/null +++ b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "Should cluster an mmseqs database": { + "content": [ + [ + "test_output_cluster.0", + "test_output_cluster.1", + "test_output_cluster.dbtype", + "test_output_cluster.index" + ], + [ + "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089", + "test_output_cluster.index:md5,ca7e1f0967222b06d7e05e47bcbe1e50" + ], + "versions.yml:md5,4acad55952c6d1fb41ad7f5a44468aed" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-05T10:44:45.713270981" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/mmseqs/cluster/nextflow.config b/modules/nf-core/mmseqs/cluster/tests/nextflow.config similarity index 66% rename from tests/modules/nf-core/mmseqs/cluster/nextflow.config rename to modules/nf-core/mmseqs/cluster/tests/nextflow.config index 7513694f7a0..a43cb1807e3 100644 --- a/tests/modules/nf-core/mmseqs/cluster/nextflow.config +++ b/modules/nf-core/mmseqs/cluster/tests/nextflow.config @@ -1,7 +1,4 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: UNTAR { publishDir = [ enabled : false ] } @@ -10,5 +7,4 @@ process { ext.prefix = "test_output_cluster" ext.args = '--remove-tmp-files 1 -v 3 ' } - } diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml index 18547591a2e..235ad03ad82 100644 --- a/modules/nf-core/mmseqs/createdb/environment.yml +++ b/modules/nf-core/mmseqs/createdb/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=15.6f452 + - bioconda::mmseqs2=16.747c6 diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf index 9487e5bcdf2..b1d6caf0b06 100644 --- a/modules/nf-core/mmseqs/createdb/main.nf +++ b/modules/nf-core/mmseqs/createdb/main.nf @@ -4,8 +4,8 @@ process MMSEQS_CREATEDB { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': + 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" input: tuple val(meta), path(sequence) diff --git a/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap index a24c4118002..92f1e6d8257 100644 --- a/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,e644cbe263d4560298438a24f268eb6f" + "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-08-09T10:01:44.163384" + "timestamp": "2024-12-05T10:35:27.322864475" }, "Should build an mmseqs db from a zipped amino acid sequence file": { "content": [ @@ -49,13 +49,13 @@ ] ], [ - "versions.yml:md5,e644cbe263d4560298438a24f268eb6f" + "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-08-09T10:01:48.894044" + "timestamp": "2024-12-05T10:35:33.418552595" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createdb/tests/tags.yml b/modules/nf-core/mmseqs/createdb/tests/tags.yml deleted file mode 100644 index 1f511ab0bfe..00000000000 --- a/modules/nf-core/mmseqs/createdb/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mmseqs/createdb: - - modules/nf-core/mmseqs/createdb/** diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index 18547591a2e..235ad03ad82 100644 --- a/modules/nf-core/mmseqs/createtsv/environment.yml +++ b/modules/nf-core/mmseqs/createtsv/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=15.6f452 + - bioconda::mmseqs2=16.747c6 diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf index dcd4c13d3cd..d5afc0694ae 100644 --- a/modules/nf-core/mmseqs/createtsv/main.nf +++ b/modules/nf-core/mmseqs/createtsv/main.nf @@ -5,8 +5,8 @@ process MMSEQS_CREATETSV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': + 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" input: tuple val(meta), path(db_result) diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap index 1087de88d55..6192fa16a83 100644 --- a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ], "tsv": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-12T13:55:17.642787" + "timestamp": "2024-12-05T10:50:48.386202112" }, "mmseqs/createtsv - sarscov2 - cluster - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ], "tsv": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-12T13:55:33.645454" + "timestamp": "2024-12-05T10:50:56.33475153" }, "mmseqs/createtsv - bacteroides_fragilis - taxonomy": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ], "tsv": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-12T13:54:45.718678" + "timestamp": "2024-12-05T11:25:54.741775111" }, "mmseqs/createtsv - sarscov2 - cluster": { "content": [ @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ], "tsv": [ [ @@ -129,14 +129,14 @@ ] ], "versions": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-12T13:55:02.731974" + "timestamp": "2024-12-05T10:50:42.432284995" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createtsv/tests/tags.yml b/modules/nf-core/mmseqs/createtsv/tests/tags.yml deleted file mode 100644 index e27827f58aa..00000000000 --- a/modules/nf-core/mmseqs/createtsv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mmseqs/createtsv: - - "modules/nf-core/mmseqs/createtsv/**" diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index 18547591a2e..235ad03ad82 100644 --- a/modules/nf-core/mmseqs/databases/environment.yml +++ b/modules/nf-core/mmseqs/databases/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=15.6f452 + - bioconda::mmseqs2=16.747c6 diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf index d43681cea94..176d7b45d59 100644 --- a/modules/nf-core/mmseqs/databases/main.nf +++ b/modules/nf-core/mmseqs/databases/main.nf @@ -4,8 +4,8 @@ process MMSEQS_DATABASES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': + 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" input: val database diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap index 00d3003ebbc..b3d0b9f7636 100644 --- a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap @@ -15,14 +15,14 @@ "database_taxonomy" ], [ - "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4" + "versions.yml:md5,e236ec16fdc9f054d0a660d02e680255" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-09-06T15:43:58.454012" + "timestamp": "2024-12-05T14:33:16.697954954" }, "test-mmseqs-databases-stub": { "content": [ diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml index 18547591a2e..235ad03ad82 100644 --- a/modules/nf-core/mmseqs/linclust/environment.yml +++ b/modules/nf-core/mmseqs/linclust/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=15.6f452 + - bioconda::mmseqs2=16.747c6 diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf index 7453c263d38..c5927985897 100644 --- a/modules/nf-core/mmseqs/linclust/main.nf +++ b/modules/nf-core/mmseqs/linclust/main.nf @@ -4,8 +4,8 @@ process MMSEQS_LINCLUST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': + 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" input: tuple val(meta), path(db_input) diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap index 4d7fb8b1050..e1622d49d12 100644 --- a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap @@ -11,12 +11,12 @@ "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089", "test_output_cluster.index:md5,38908275cdd5727ae0eb9be017f9ca13" ], - "versions.yml:md5,65ce4e8b36259f881d11b0d8caaee69a" + "versions.yml:md5,969cb26241f66ac758c104f9561860b1" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-08-13T10:40:19.482219" + "timestamp": "2024-12-05T10:43:26.020522437" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/linclust/tests/tags.yml b/modules/nf-core/mmseqs/linclust/tests/tags.yml deleted file mode 100644 index 4aa9f308abe..00000000000 --- a/modules/nf-core/mmseqs/linclust/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mmseqs/linclust: - - modules/nf-core/mmseqs/linclust/** diff --git a/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test.snap b/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test.snap index 72cef79dcf3..139b7abcd54 100644 --- a/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test.snap +++ b/subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test.snap @@ -2,10 +2,10 @@ "mmseqs_contig_taxonomy - bacteroides_fragilis - contig": { "content": [ [ - "versions.yml:md5,394dfc0a2af83eb4c8ec9e180cb44b37", - "versions.yml:md5,49890601bcc79306ea202d0901d0578e", - "versions.yml:md5,50d8f191f53c3da260e67aa3ca64fd77", - "versions.yml:md5,b74ec13e6b0d418f76a233963be3c61c" + "versions.yml:md5,5d88d2bec706c621fc1708057d96ba4b", + "versions.yml:md5,b74ec13e6b0d418f76a233963be3c61c", + "versions.yml:md5,cb8267097608050e1f9a1d18aca1637a", + "versions.yml:md5,e23563c111847451013d166d17b8a0b4" ], true, [ @@ -18,9 +18,9 @@ "mmseqs_database" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-05-17T11:25:44.10208454" + "timestamp": "2024-12-05T14:55:07.144815554" } -} +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index fd8d258697b..019ad006b8c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -359,9 +359,6 @@ mitohifi/findmitoreference: mitohifi/mitohifi: - modules/nf-core/mitohifi/mitohifi/** - tests/modules/nf-core/mitohifi/mitohifi/** -mmseqs/cluster: - - modules/nf-core/mmseqs/cluster/** - - tests/modules/nf-core/mmseqs/cluster/** mmseqs/easysearch: - modules/nf-core/mmseqs/easysearch/** - tests/modules/nf-core/mmseqs/easysearch/** diff --git a/tests/modules/nf-core/mmseqs/cluster/main.nf b/tests/modules/nf-core/mmseqs/cluster/main.nf deleted file mode 100644 index 5adb4da806a..00000000000 --- a/tests/modules/nf-core/mmseqs/cluster/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' -include { MMSEQS_CLUSTER } from '../../../../../modules/nf-core/mmseqs/cluster/main.nf' - -workflow test_mmseqs_cluster { - - input = [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['genome']['mmseqs_tar_gz'], checkIfExists: true) - ] - - ch_db = UNTAR ( input ).untar - - MMSEQS_CLUSTER ( ch_db ) - -} diff --git a/tests/modules/nf-core/mmseqs/cluster/test.yml b/tests/modules/nf-core/mmseqs/cluster/test.yml deleted file mode 100644 index 88eb64c4cf6..00000000000 --- a/tests/modules/nf-core/mmseqs/cluster/test.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: mmseqs cluster test_mmseqs_cluster - command: nextflow run ./tests/modules/nf-core/mmseqs/cluster -entry test_mmseqs_cluster -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mmseqs/cluster/nextflow.config - tags: - - mmseqs/cluster - - mmseqs - files: - - path: output/mmseqs/test_output_cluster/test_output_cluster.0 - - path: output/mmseqs/test_output_cluster/test_output_cluster.1 - - path: output/mmseqs/test_output_cluster/test_output_cluster.dbtype - - path: output/mmseqs/test_output_cluster/test_output_cluster.index - - path: output/mmseqs/versions.yml