From c2f44fe8c5999142d34119220b6591475eb953f5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 16 Jan 2024 09:02:19 +0100 Subject: [PATCH] Fix BUSCO download links due to deprecation of old verison of db in tests --- conf/test.config | 2 +- conf/test_adapterremoval.config | 2 +- conf/test_ancient_dna.config | 2 +- conf/test_bbnorm.config | 2 +- conf/test_binrefinement.config | 2 +- conf/test_host_rm.config | 2 +- conf/test_hybrid.config | 2 +- nextflow_schema.json | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/test.config b/conf/test.config index 9c93278f..43a7f18a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,7 +26,7 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" busco_clean = true skip_gtdbtk = true skip_concoct = true diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config index d8bd581a..dc00d319 100644 --- a/conf/test_adapterremoval.config +++ b/conf/test_adapterremoval.config @@ -27,7 +27,7 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" skip_gtdbtk = true clip_tool = 'adapterremoval' skip_concoct = true diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config index ea672651..bc441be8 100644 --- a/conf/test_ancient_dna.config +++ b/conf/test_ancient_dna.config @@ -26,7 +26,7 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" skip_gtdbtk = true ancient_dna = true binning_map_mode = 'own' diff --git a/conf/test_bbnorm.config b/conf/test_bbnorm.config index 55d48a8b..02e764c3 100644 --- a/conf/test_bbnorm.config +++ b/conf/test_bbnorm.config @@ -32,7 +32,7 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" busco_clean = true skip_gtdbtk = true bbnorm = true diff --git a/conf/test_binrefinement.config b/conf/test_binrefinement.config index bc1796d5..79105ec4 100644 --- a/conf/test_binrefinement.config +++ b/conf/test_binrefinement.config @@ -27,7 +27,7 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" skip_gtdbtk = true refine_bins_dastool = true refine_bins_dastool_threshold = 0 diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config index 7af3bcd4..30cae576 100644 --- a/conf/test_host_rm.config +++ b/conf/test_host_rm.config @@ -24,7 +24,7 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.host_rm.csv' min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" skip_gtdbtk = true skip_concoct = true } diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config index 0600c88c..3ca0608e 100644 --- a/conf/test_hybrid.config +++ b/conf/test_hybrid.config @@ -23,7 +23,7 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.hybrid.csv' min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" + busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz" skip_gtdbtk = true skip_concoct = true } diff --git a/nextflow_schema.json b/nextflow_schema.json index 13f7e6bc..99d30c06 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -763,7 +763,7 @@ "busco_db": { "type": "string", "description": "Download URL for BUSCO lineage dataset, or path to a tar.gz archive, or local directory containing already downloaded and unpacked lineage datasets.", - "help_text": "E.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz or '/path/to/buscodb' (files still need to be unpacked manually). Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/." + "help_text": "E.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz or '/path/to/buscodb' (files still need to be unpacked manually). Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/." }, "busco_auto_lineage_prok": { "type": "boolean",