From 75578b9bb5a0d5f98498c212000fa7704185461e Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 20 Jan 2025 18:23:58 +0100 Subject: [PATCH] Update all mmseqs modules to version 17 --- .../nf-core/mmseqs/cluster/environment.yml | 2 +- modules/nf-core/mmseqs/cluster/main.nf | 4 +- .../mmseqs/cluster/tests/main.nf.test.snap | 6 +-- .../nf-core/mmseqs/createdb/environment.yml | 2 +- modules/nf-core/mmseqs/createdb/main.nf | 4 +- .../mmseqs/createdb/tests/main.nf.test.snap | 12 ++--- .../mmseqs/createindex/environment.yml | 2 +- modules/nf-core/mmseqs/createindex/main.nf | 4 +- .../createindex/tests/main.nf.test.snap | 12 ++--- .../nf-core/mmseqs/createtsv/environment.yml | 2 +- modules/nf-core/mmseqs/createtsv/main.nf | 4 +- .../mmseqs/createtsv/tests/main.nf.test.snap | 44 ++++++++++++------- .../nf-core/mmseqs/databases/environment.yml | 2 +- modules/nf-core/mmseqs/databases/main.nf | 4 +- .../mmseqs/databases/tests/main.nf.test.snap | 6 +-- .../nf-core/mmseqs/easysearch/environment.yml | 2 +- modules/nf-core/mmseqs/easysearch/main.nf | 4 +- .../mmseqs/easysearch/tests/main.nf.test.snap | 6 +-- .../nf-core/mmseqs/linclust/environment.yml | 2 +- modules/nf-core/mmseqs/linclust/main.nf | 4 +- .../mmseqs/linclust/tests/main.nf.test.snap | 6 +-- modules/nf-core/mmseqs/search/environment.yml | 2 +- modules/nf-core/mmseqs/search/main.nf | 4 +- .../mmseqs/search/tests/main.nf.test.snap | 12 ++--- .../nf-core/mmseqs/taxonomy/environment.yml | 2 +- modules/nf-core/mmseqs/taxonomy/main.nf | 4 +- .../mmseqs/taxonomy/tests/main.nf.test.snap | 14 +++--- .../mmseqs/tsv2exprofiledb/environment.yml | 2 +- .../nf-core/mmseqs/tsv2exprofiledb/main.nf | 4 +- .../tsv2exprofiledb/tests/main.nf.test.snap | 8 ++-- 30 files changed, 99 insertions(+), 87 deletions(-) diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml index 235ad03ad82..c79df337d73 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=16.747c6 + - bioconda::mmseqs2=17.b804f \ No newline at end of file diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf index b7fa6c4d2cf..f273ce8fa5f 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/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" input: tuple val(meta), path(db_input) diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap index f61bc9f3070..09bc83f6bb0 100644 --- a/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap @@ -11,12 +11,12 @@ "test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd", "test_output_cluster.index:md5,9848b52b6df827d80a04f7c71c50056b" ], - "versions.yml:md5,4acad55952c6d1fb41ad7f5a44468aed" + "versions.yml:md5,8cd8fdc3e9d128b0a4dc634b8748c213" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-15T19:30:14.704271821" + "timestamp": "2025-01-20T14:07:52.454357" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml index 235ad03ad82..d3561349025 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=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf index ef11306895b..6f8d5b15b20 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/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" 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 ececa7a4dd5..9eee149ba1f 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,d30a1af41e7f3f5b67afdec412fa693f" + "versions.yml:md5,c62b08152082097334109fe08ec6333a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-15T19:30:25.339409238" + "timestamp": "2025-01-20T14:11:57.883871" }, "Should build an mmseqs db from a zipped amino acid sequence file": { "content": [ @@ -49,13 +49,13 @@ ] ], [ - "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f" + "versions.yml:md5,c62b08152082097334109fe08ec6333a" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-15T19:30:34.93361715" + "timestamp": "2025-01-20T14:12:10.986433" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml index 235ad03ad82..d3561349025 100644 --- a/modules/nf-core/mmseqs/createindex/environment.yml +++ b/modules/nf-core/mmseqs/createindex/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf index facc9a673f2..1da528d4556 100644 --- a/modules/nf-core/mmseqs/createindex/main.nf +++ b/modules/nf-core/mmseqs/createindex/main.nf @@ -4,8 +4,8 @@ process MMSEQS_CREATEINDEX { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0' - : 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0'}" + ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1' + : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}" input: tuple val(meta), path(db) diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap index 2df31248b79..f18d49dd1fd 100644 --- a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,227ad351b62984329aabf90242522eee" + "versions.yml:md5,9745ec52ea0356d97ef2f5c18c01d7e7" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T13:17:27.724764877" + "timestamp": "2025-01-20T17:15:56.23597" }, "createindex_filtered_files": { "content": [ @@ -18,7 +18,7 @@ "mmseqs.dbtype:md5,f1d3ff8443297732862df21dc4e57262", "mmseqs.fasta:md5,b40600ad3be77f076df716e6cf99c64c", "mmseqs.idx.dbtype:md5,9a198d4f48144e20661df7fd2dc41bf7", - "mmseqs.idx.index:md5,deac42b3a049a1c8a251d81b6b9538c9", + "mmseqs.idx.index:md5,7c1dc5d8044ab7e0535d0ba4d7b7ab07", "mmseqs.index:md5,c012bdab1c61eeafcb99d1b26650f3d0", "mmseqs.lookup:md5,fa898551a6b303614ae6e29c237b7fc6", "mmseqs.source:md5,16bef02c30aadbfa8d035596502f0aa2", @@ -54,9 +54,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-07-09T10:43:46.077636" + "timestamp": "2025-01-20T17:15:56.186115" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index 235ad03ad82..d3561349025 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=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf index b41b5c54a65..3ab0159aebc 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/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" 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 8279c81e6dd..a70f839fb9e 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:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ], "tsv": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-05T10:50:48.386202112" + "timestamp": "2025-01-20T17:29:15.220926" }, "mmseqs/createtsv - sarscov2 - cluster - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ], "tsv": [ [ @@ -59,30 +59,42 @@ ] ], "versions": [ - "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-05T10:50:56.33475153" + "timestamp": "2025-01-20T17:29:32.089204" }, "mmseqs/createtsv - bacteroides_fragilis - taxonomy": { "content": [ { "0": [ - + [ + { + "id": "test_query", + "single_end": false + }, + "test_query.tsv:md5,9179f5c85b8b87a4dc998c9d17840161" + ] ], "1": [ - + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ], "tsv": [ - + [ + { + "id": "test_query", + "single_end": false + }, + "test_query.tsv:md5,9179f5c85b8b87a4dc998c9d17840161" + ] ], "versions": [ - + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ] } ], @@ -90,7 +102,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T14:29:41.214561285" + "timestamp": "2025-01-20T17:28:41.472818" }, "mmseqs/createtsv - sarscov2 - cluster": { "content": [ @@ -105,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ], "tsv": [ [ @@ -117,7 +129,7 @@ ] ], "versions": [ - "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7" + "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77" ] } ], @@ -125,6 +137,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-15T11:17:04.119521629" + "timestamp": "2025-01-20T17:28:58.633976" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index 235ad03ad82..d3561349025 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=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf index 8f94eac5ffa..51d54ab764c 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/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" 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 b3d0b9f7636..2805e1c025f 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,e236ec16fdc9f054d0a660d02e680255" + "versions.yml:md5,387bbb2d1d6bac273e8158743af4c856" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-05T14:33:16.697954954" + "timestamp": "2025-01-20T15:32:42.284982" }, "test-mmseqs-databases-stub": { "content": [ diff --git a/modules/nf-core/mmseqs/easysearch/environment.yml b/modules/nf-core/mmseqs/easysearch/environment.yml index 235ad03ad82..d3561349025 100644 --- a/modules/nf-core/mmseqs/easysearch/environment.yml +++ b/modules/nf-core/mmseqs/easysearch/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/easysearch/main.nf b/modules/nf-core/mmseqs/easysearch/main.nf index 14e3c684c38..bfc5e45ff9d 100644 --- a/modules/nf-core/mmseqs/easysearch/main.nf +++ b/modules/nf-core/mmseqs/easysearch/main.nf @@ -4,8 +4,8 @@ process MMSEQS_EASYSEARCH { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0' - : 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0'}" + ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1' + : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap b/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap index 9f789c7121e..b56170f546a 100644 --- a/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,2486965fbe4dca06ebf5bc84782dec83" + "versions.yml:md5,0459b89b5e5e838b3d5ee718443e08da" ], "tsv": [ [ @@ -24,7 +24,7 @@ ] ], "versions": [ - "versions.yml:md5,2486965fbe4dca06ebf5bc84782dec83" + "versions.yml:md5,0459b89b5e5e838b3d5ee718443e08da" ] } ], @@ -32,7 +32,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T14:14:22.925002111" + "timestamp": "2025-01-20T18:11:14.000659" }, "sarscov2 - illumina - contigs - fasta - stub": { "content": [ diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml index 235ad03ad82..d3561349025 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=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf index fb8663b98f1..987108b3945 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/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" 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 b5f555b847a..ab999b3f53e 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,b9d9c6dbc098c97ae446f612efd8eafd", "test_output_cluster.index:md5,a0b78f31aee2c327d72f32919814baf1" ], - "versions.yml:md5,969cb26241f66ac758c104f9561860b1" + "versions.yml:md5,acd9806d081cf15f08f26263bd9dfe80" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-15T19:38:00.258247122" + "timestamp": "2025-01-20T18:13:05.966684" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/search/environment.yml b/modules/nf-core/mmseqs/search/environment.yml index 235ad03ad82..d3561349025 100644 --- a/modules/nf-core/mmseqs/search/environment.yml +++ b/modules/nf-core/mmseqs/search/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/search/main.nf b/modules/nf-core/mmseqs/search/main.nf index 73cc8a7af68..31892f59125 100644 --- a/modules/nf-core/mmseqs/search/main.nf +++ b/modules/nf-core/mmseqs/search/main.nf @@ -4,8 +4,8 @@ process MMSEQS_SEARCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" input: tuple val(meta), path(db_query) diff --git a/modules/nf-core/mmseqs/search/tests/main.nf.test.snap b/modules/nf-core/mmseqs/search/tests/main.nf.test.snap index 746588b6ea5..3231487c88e 100644 --- a/modules/nf-core/mmseqs/search/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/search/tests/main.nf.test.snap @@ -9,7 +9,7 @@ ], { "MMSEQS_SEARCH": { - "mmseqs": "16.747c6" + "mmseqs": "17.b804f" } } ], @@ -17,7 +17,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T14:16:15.879855065" + "timestamp": "2025-01-20T18:14:57.259665" }, "sarscov2 - test-search - stub": { "content": [ @@ -45,7 +45,7 @@ ] ], "1": [ - "versions.yml:md5,0c09b7c1276ab675bbf641afaeac482b" + "versions.yml:md5,55da7c5f326efc78452de61273aaed5b" ], "db_search": [ [ @@ -70,12 +70,12 @@ ] ], "versions": [ - "versions.yml:md5,0c09b7c1276ab675bbf641afaeac482b" + "versions.yml:md5,55da7c5f326efc78452de61273aaed5b" ] }, { "MMSEQS_SEARCH": { - "mmseqs": "16.747c6" + "mmseqs": "17.b804f" } } ], @@ -83,6 +83,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T14:16:22.186243162" + "timestamp": "2025-01-20T18:15:12.804291" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/taxonomy/environment.yml b/modules/nf-core/mmseqs/taxonomy/environment.yml index c5b78bc7d80..69afa609565 100644 --- a/modules/nf-core/mmseqs/taxonomy/environment.yml +++ b/modules/nf-core/mmseqs/taxonomy/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mmseqs2=16.747c6" + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/taxonomy/main.nf b/modules/nf-core/mmseqs/taxonomy/main.nf index bb0caf23be6..d73bf03fc0d 100644 --- a/modules/nf-core/mmseqs/taxonomy/main.nf +++ b/modules/nf-core/mmseqs/taxonomy/main.nf @@ -4,8 +4,8 @@ process MMSEQS_TAXONOMY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0': - 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }" + 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1': + 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }" input: tuple val(meta), path(db_query) diff --git a/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test.snap b/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test.snap index 8a21ce4f9b2..4402c7312b9 100644 --- a/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/taxonomy/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "test_query.index" ], [ - "versions.yml:md5,a8f24dca956a1c84099ff129f826c63f" + "versions.yml:md5,d86f3223ff4a4d664228707b581dca8a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-08-09T10:11:53.632751" + "timestamp": "2025-01-20T16:28:40.091017" }, "mmseqs/taxonomy - bacteroides_fragilis - genome_nt - stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,019af282b55a28b89c5376b4e7a70fe4" + "versions.yml:md5,d86f3223ff4a4d664228707b581dca8a" ], "db_taxonomy": [ [ @@ -100,7 +100,7 @@ ] ], "versions": [ - "versions.yml:md5,019af282b55a28b89c5376b4e7a70fe4" + "versions.yml:md5,d86f3223ff4a4d664228707b581dca8a" ] } ], @@ -108,6 +108,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T12:52:06.466899117" + "timestamp": "2025-01-20T16:48:57.634552" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml index 235ad03ad82..d3561349025 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=16.747c6 + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/main.nf b/modules/nf-core/mmseqs/tsv2exprofiledb/main.nf index b64f00fad5f..086898fb266 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/main.nf +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/main.nf @@ -4,8 +4,8 @@ process MMSEQS_TSV2EXPROFILEDB { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0' - : 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0'}" + ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1' + : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}" input: path database diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/tsv2exprofiledb/tests/main.nf.test.snap index 10de97a47ed..d91350e8dce 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/tests/main.nf.test.snap @@ -55,14 +55,14 @@ "tmp" ], [ - "versions.yml:md5,b5bfad51f25a7fb9add496eb09c5f2b2" + "versions.yml:md5,8865a91acd412cbac3add1a236c78ee2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T06:32:24.126939413" + "timestamp": "2025-01-20T18:17:10.037107" }, "sarscov2 - db": { "content": [ @@ -137,13 +137,13 @@ "tmp" ], [ - "versions.yml:md5,b5bfad51f25a7fb9add496eb09c5f2b2" + "versions.yml:md5,8865a91acd412cbac3add1a236c78ee2" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T06:32:11.496679278" + "timestamp": "2025-01-20T18:16:54.792553" } } \ No newline at end of file