From cd0495b144f245164831d518d4a2c8428d462f17 Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Thu, 12 Dec 2024 18:01:58 -0300 Subject: [PATCH] Update versions --- modules/nf-core/busco/busco/main.nf | 4 +++- modules/nf-core/busco/busco/meta.yml | 8 ++++---- .../busco/busco/tests/main.nf.test.snap | 4 ++-- .../nf-core/busco/generateplot/environment.yml | 5 ++--- modules/nf-core/busco/generateplot/main.nf | 4 ++-- .../busco/generateplot/tests/main.nf.test.snap | 18 +++++++++--------- .../tests/main.nf.test.snap | 8 ++++---- 7 files changed, 26 insertions(+), 25 deletions(-) diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf index 8d62d000731d..27ab2fd7e8d3 100644 --- a/modules/nf-core/busco/busco/main.nf +++ b/modules/nf-core/busco/busco/main.nf @@ -24,7 +24,9 @@ process BUSCO_BUSCO { tuple val(meta), path("*-busco/*/run_*/busco_sequences") , emit: seq_dir , optional: true tuple val(meta), path("*-busco/*/translated_proteins") , emit: translated_dir , optional: true tuple val(meta), path("*-busco") , emit: busco_dir - tuple val(meta), path("busco_downloads") , emit: busco_downloads_dir , optional: true + tuple val(meta), path("busco_downloads/lineages/*") , emit: downloaded_lineages , optional: true + tuple val(meta), path("busco_downloads/lineages/*") , emit: downloaded_lineages , optional: true + path "versions.yml" , emit: versions when: diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml index ec535637a0a8..cbeb3a1f6a78 100644 --- a/modules/nf-core/busco/busco/meta.yml +++ b/modules/nf-core/busco/busco/meta.yml @@ -132,16 +132,16 @@ output: type: directory description: BUSCO lineage specific output pattern: "*-busco" - - busco_downloads_dir: + - busco_downloaded_lineages: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "busco_downloads": + - "busco_downloads/lineages/*": type: directory - description: BUSCO downloads directory - pattern: "busco_downloads" + description: BUSCO lineages downloaded + pattern: "busco_downloads/lineages/*" - versions: - versions.yml: type: file diff --git a/modules/nf-core/busco/busco/tests/main.nf.test.snap b/modules/nf-core/busco/busco/tests/main.nf.test.snap index cf92edab657f..38d04476b6f7 100644 --- a/modules/nf-core/busco/busco/tests/main.nf.test.snap +++ b/modules/nf-core/busco/busco/tests/main.nf.test.snap @@ -84,7 +84,7 @@ ] ] ], - "busco_downloads_dir": [ + "downloaded_lineages": [ ], "full_table": [ @@ -124,7 +124,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-12-12T13:52:55.9049764" + "timestamp": "2024-12-12T17:53:12.04195472" }, "test_busco_eukaryote_augustus": { "content": [ diff --git a/modules/nf-core/busco/generateplot/environment.yml b/modules/nf-core/busco/generateplot/environment.yml index 766c0f406b07..53e5e90e394a 100644 --- a/modules/nf-core/busco/generateplot/environment.yml +++ b/modules/nf-core/busco/generateplot/environment.yml @@ -1,7 +1,6 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::busco=5.7.1 + - bioconda::busco=5.8.2 diff --git a/modules/nf-core/busco/generateplot/main.nf b/modules/nf-core/busco/generateplot/main.nf index 6a4b339318b9..7411040bf2e4 100644 --- a/modules/nf-core/busco/generateplot/main.nf +++ b/modules/nf-core/busco/generateplot/main.nf @@ -3,8 +3,8 @@ process BUSCO_GENERATEPLOT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0': - 'biocontainers/busco:5.7.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0': + 'biocontainers/busco:5.8.2--pyhdfd78af_0' }" input: path short_summary_txt, stageAs: 'busco/*' diff --git a/modules/nf-core/busco/generateplot/tests/main.nf.test.snap b/modules/nf-core/busco/generateplot/tests/main.nf.test.snap index d9773ec6268c..4b9d688b7d63 100644 --- a/modules/nf-core/busco/generateplot/tests/main.nf.test.snap +++ b/modules/nf-core/busco/generateplot/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74" + "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T15:40:01.523993" + "timestamp": "2024-12-12T17:44:49.021631034" }, "stub": { "content": [ @@ -18,20 +18,20 @@ "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e" ], "1": [ - "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74" + "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6" ], "png": [ "busco_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e" ], "versions": [ - "versions.yml:md5,726fa3440ea3a0b2e9d032d7e4d25e74" + "versions.yml:md5,de6313bd06a673b9db4a982abf9019e6" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T15:40:11.864276" + "timestamp": "2024-12-12T17:44:57.632273743" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap index 5ae259f2a728..175de42ca94a 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap @@ -239,17 +239,17 @@ ] ], [ - "versions.yml:md5,05d8022e3afb0d5642ed17147b991730", - "versions.yml:md5,53987b35fc275297efdaf525937fdca3", "versions.yml:md5,624e4661a636558db4521457fcddf6dd", "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a", - "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64" + "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64", + "versions.yml:md5,ab3572b594228efec5824329cba08997", + "versions.yml:md5,b717797e52f95b2e9d5fb139f7c1e8ac" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-12-11T12:47:41.989229128" + "timestamp": "2024-12-12T17:45:57.908942636" } } \ No newline at end of file