diff --git a/modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/busco/environment.yml index 5b918b45b2d..53e5e90e394 100644 --- a/modules/nf-core/busco/busco/environment.yml +++ b/modules/nf-core/busco/busco/environment.yml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::busco=5.7.1 + - bioconda::busco=5.8.2 diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf index f7c1a662d3e..9b31904d1c5 100644 --- a/modules/nf-core/busco/busco/main.nf +++ b/modules/nf-core/busco/busco/main.nf @@ -4,14 +4,14 @@ process BUSCO_BUSCO { 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: tuple val(meta), path(fasta, stageAs:'tmp_input/*') val mode // Required: One of genome, proteins, or transcriptome - val lineage // Required: lineage to check against, "auto" enables --auto-lineage instead - path busco_lineages_path // Recommended: path to busco lineages - downloads if not set + val lineage // Required: lineage for checking against, or "auto/auto_prok/auto_euk" for enabling auto-lineage + path busco_lineages_path // Recommended: busco lineages file - downloads if not set path config_file // Optional: busco configuration file output: @@ -35,8 +35,10 @@ process BUSCO_BUSCO { } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}-${lineage}" - def busco_config = config_file ? "--config $config_file" : '' - def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}" + def busco_config = config_file ? "--config ${config_file}" : '' + def busco_lineage = lineage in [ 'auto', 'auto_prok', 'auto_euk'] + ? lineage.replaceFirst('auto', '--auto-lineage').replaceAll('_', '-') + : "--lineage_dataset ${lineage}" def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : '' """ # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml index 7cb6d69c184..9076b8c43e0 100644 --- a/modules/nf-core/busco/busco/meta.yml +++ b/modules/nf-core/busco/busco/meta.yml @@ -32,7 +32,8 @@ input: pattern: "{genome,proteins,transcriptome}" - - lineage: type: string - description: The BUSCO lineage to use, or "auto" to automatically select lineage + description: The BUSCO lineage to use, or "auto", "auto_prok" or "auto_euk" + to automatically select lineage - - busco_lineages_path: type: directory description: Path to local BUSCO lineages directory. diff --git a/modules/nf-core/busco/busco/tests/main.nf.test b/modules/nf-core/busco/busco/tests/main.nf.test index bb7b49a97c4..7aa131fccc0 100644 --- a/modules/nf-core/busco/busco/tests/main.nf.test +++ b/modules/nf-core/busco/busco/tests/main.nf.test @@ -21,7 +21,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) ] input[1] = 'genome' - input[2] = 'bacteria_odb10' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues + input[2] = 'bacteria_odb12' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues input[3] = [] // Download busco lineage input[4] = [] // No config """ @@ -85,7 +85,7 @@ nextflow_process { ] ] input[1] = 'genome' - input[2] = 'bacteria_odb10' + input[2] = 'bacteria_odb12' input[3] = [] input[4] = [] """ @@ -126,7 +126,6 @@ nextflow_process { } assert snapshot( - process.out.batch_summary[0][1], process.out.full_table[0][1], process.out.missing_busco_list[0][1], process.out.versions[0] @@ -274,7 +273,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true) ] input[1] = 'proteins' - input[2] = 'bacteria_odb10' + input[2] = 'bacteria_odb12' input[3] = [] input[4] = [] """ @@ -336,7 +335,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) ] input[1] = 'transcriptome' - input[2] = 'bacteria_odb10' + input[2] = 'bacteria_odb12' input[3] = [] input[4] = [] """ @@ -397,7 +396,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) ] input[1] = 'genome' - input[2] = 'bacteria_odb10' + input[2] = 'bacteria_odb12' input[3] = [] input[4] = [] """ @@ -412,4 +411,4 @@ nextflow_process { } } -} +} \ No newline at end of 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 1b6411bcec7..a177c48e3d4 100644 --- a/modules/nf-core/busco/busco/tests/main.nf.test.snap +++ b/modules/nf-core/busco/busco/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -55,14 +55,14 @@ ] ], "9": [ - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "batch_summary": [ [ { "id": "test" }, - "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "busco_dir": [ @@ -110,121 +110,141 @@ ], "versions": [ - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:28:04.451297" + "timestamp": "2024-12-11T12:45:52.045550047" }, "test_busco_eukaryote_augustus": { "content": [ "test-eukaryota_odb10-busco.batch_summary.txt:md5,3ea3bdc423a461dae514d816bdc61c89", - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:26:36.974986" + "timestamp": "2024-12-11T13:07:45.550722277" }, "test_busco_genome_single_fasta": { "content": [ - "test-bacteria_odb10-busco.batch_summary.txt:md5,21b3fb771cf36be917cc451540d999be", - "full_table.tsv:md5,638fe7590f442c57361554dae330eca1", - "missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a", - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "test-bacteria_odb12-busco.batch_summary.txt:md5,e3e503e1540b633d95c273c465945740", + "full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7", + "missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0", + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:22:45.07816" + "timestamp": "2024-12-11T12:43:40.359736221" }, "test_busco_genome_multi_fasta": { "content": [ - "test-bacteria_odb10-busco.batch_summary.txt:md5,fcd3c208913e8abda3d6742c43fec5fa", [ - "full_table.tsv:md5,c657edcc7d0de0175869717551df6e83", - "full_table.tsv:md5,638fe7590f442c57361554dae330eca1" + "full_table.tsv:md5,5e7df014f2804789f0d98ae2e09734ad", + "full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7" ], [ - "missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112", - "missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a" + "missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50", + "missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0" ], - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:23:50.255602" + "timestamp": "2024-12-11T17:17:42.175675858" }, "test_busco_eukaryote_metaeuk": { "content": [ "test-eukaryota_odb10-busco.batch_summary.txt:md5,ff6d8277e452a83ce9456bbee666feb6", - "full_table.tsv:md5,92b1b1d5cb5ea0e2093d16f00187e8c7", - "missing_busco_list.tsv:md5,0352e563de290bf804c708323c35a9e3", - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "full_table.tsv:md5,9bfa9ef7d54ca6ad8bcf8e87729720b1", + "missing_busco_list.tsv:md5,325b529e5a8af2a392d747b4eddc150c", + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:25:38.159041" + "timestamp": "2024-12-11T13:07:17.335085326" }, "test_busco_transcriptome": { "content": [ - "test-bacteria_odb10-busco.batch_summary.txt:md5,8734b3f379c4c0928e5dd4ea1873dc64", - "full_table.tsv:md5,1b2ce808fdafa744c56b5f781551272d", - "missing_busco_list.tsv:md5,a6931b6470262b997b8b99ea0f1d14a4", + "test-bacteria_odb12-busco.batch_summary.txt:md5,6cd69d8a66b5f8b7fd4a9de758e7a739", + "full_table.tsv:md5,73a3a90c2fa8fef41cafed5a607fab66", + "missing_busco_list.tsv:md5,4778855c345f4e409750c9bbd38c5a0c", [ - "1024388at2.faa:md5,797d603d262a6595a112e25b73e878b0", - "1054741at2.faa:md5,cd4b928cba6b19b4437746ba507e7195", - "1093223at2.faa:md5,df9549708e5ffcfaee6a74dd70a0e5dc", - "1151822at2.faa:md5,12726afc1cdc40c13392e1596e93df3a", - "143460at2.faa:md5,d887431fd988a5556a523440f02d9594", - "1491686at2.faa:md5,d03362d19979b27306c192f1c74a84e5", - "1504821at2.faa:md5,4f5f6e5c57bac0092c1d85ded73d7e67", - "1574817at2.faa:md5,1153e55998c2929eacad2aed7d08d248", - "1592033at2.faa:md5,bb7a59e5f3a57ba12d10dabf4c77ab57", - "1623045at2.faa:md5,8fe38155feb1802beb97ef7714837bf5", - "1661836at2.faa:md5,6c6d592c2fbb0d7a4e5e1f47a15644f0", - "1674344at2.faa:md5,bb41b44e53565a54cadf0b780532fe08", - "1698718at2.faa:md5,f233860000028eb00329aa85236c71e5", - "1990650at2.faa:md5,34a2d29c5f8b6253159ddb7a43fa1829", - "223233at2.faa:md5,dec6705c7846c989296e73942f953cbc", - "402899at2.faa:md5,acc0f271f9a586d2ce1ee41669b22999", - "505485at2.faa:md5,aa0391f8fa5d9bd19b30d844d5a99845", - "665824at2.faa:md5,47f8ad43b6a6078206feb48c2e552793", - "776861at2.faa:md5,f8b90c13f7c6be828dea3bb920195e3d", - "874197at2.faa:md5,8d22a35a768debe6f376fc695d233a69", - "932854at2.faa:md5,2eff2de1ab83b22f3234a529a44e22bb", - "95696at2.faa:md5,247bfd1aef432f7b5456307768e9149c" + "9767721at2.faa:md5,1731738ca153959391f8302fd5a3679f", + "9778364at2.faa:md5,7a19a6b6696ae53efce30457b4dd1ab2", + "9782003at2.faa:md5,65d2a613c903852681981f8e8427dc70", + "9790352at2.faa:md5,5e18cfb68122dff7a61c5517246223fc", + "9791908at2.faa:md5,707ef4501f93a6e0dc217e037f26da54", + "9793681at2.faa:md5,e361d654145e70f06c386e75ad90f943", + "9800696at2.faa:md5,9e2f431e4aada7bdc2c317747105b874", + "9801107at2.faa:md5,83933b1426fc9abfe8891c49838cd02f", + "9801213at2.faa:md5,ec340354a86728189c3d1a294c0ccbad", + "9801753at2.faa:md5,39c09bd8a831c90aab44ded14c56d0e6", + "9802065at2.faa:md5,8361fa013dc1cd29af938c9d5ffebfe4", + "9802219at2.faa:md5,9e23aed07790f460da634f7f6132e73d", + "9802304at2.faa:md5,86b259197441716075f3d3d18f8743ba", + "9802309at2.faa:md5,b4b4613e9b69baa9274140c1b26cc27b", + "9802672at2.faa:md5,6c6d592c2fbb0d7a4e5e1f47a15644f0", + "9803420at2.faa:md5,eec6f7189ce9a596ed6ead06f2229c8a", + "9803541at2.faa:md5,132954cc7bfcb1c1fe9da105867c4b78", + "9803667at2.faa:md5,ec31d499f6b523cb081af6a3284a5a5c", + "9803773at2.faa:md5,efbe4c35075dd8c871827d4e5ac72922", + "9804006at2.faa:md5,fca5b560714ba37be0be3e2597f74c5a", + "9804243at2.faa:md5,3280570e4357fb4daedaea8a066dbf0b", + "9804478at2.faa:md5,98c2cfd8f089812a41a1e66fea630b2d", + "9804933at2.faa:md5,de648025c49061c614c77e7c9ce7ab62", + "9805026at2.faa:md5,eea9da88f3cd718514493d6890bf7660", + "9806637at2.faa:md5,c8a9e0c37a8aeb1fd44db64fd93aa3e1", + "9806651at2.faa:md5,f5abacf8930d78c81fdeb0c91c8681a7", + "9807064at2.faa:md5,1167d5c4c044b4eb82fac5d1955e7130", + "9807233at2.faa:md5,7c8adb6556a7f9a0244e7c7e5f75f20d", + "9807240at2.faa:md5,2eff2de1ab83b22f3234a529a44e22bb", + "9807458at2.faa:md5,bee695d260b2b7f8980a636fed6aa0c0", + "9808036at2.faa:md5,797ca476d2c7820151fec98d2815d6cb", + "9808348at2.faa:md5,4e8573a5d287e01aa4f5de8b48feaa42", + "9808936at2.faa:md5,30333f3f62f8e3d0ea6f6544d49572c6", + "9809052at2.faa:md5,0590efbf94fce0ad212513dcb2e8176f", + "9809084at2.faa:md5,37e6214b4204dc31858e2ef2bad5db4a", + "9809356at2.faa:md5,e18c1d5a4931a25baf7dbd1a40c417dc", + "9809796at2.faa:md5,857aac8a22c00472bfc9add7fde94c5c", + "9810191at2.faa:md5,72b63933bb045b680e0635eb03915cc0", + "9811804at2.faa:md5,da341c24e763a949d16432bb052af321", + "9812272at2.faa:md5,7a54f872dd8243c6814852d40cf1bfc0", + "9812943at2.faa:md5,149da17f067cdce328a73f6364a95b26", + "9813375at2.faa:md5,49835b9f3188434c771a840b628b07f6", + "9814755at2.faa:md5,9b4c4648d250c2e6d04acb78f9cf6df0" ], - "single_copy_proteins.faa:md5,73e2c5d6a9b0f01f2deea3cc5f21b764", - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "single_copy_proteins.faa:md5,14124def13668c6d9b0d589207754b31", + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:27:53.992893" + "timestamp": "2024-12-11T12:45:43.336777509" }, "test_busco_protein": { "content": [ - "test-bacteria_odb10-busco.batch_summary.txt:md5,f5a782378f9f94a748aa907381fdef91", - "full_table.tsv:md5,812ab6a0496fccab774643cf40c4f2a8", - "missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112", - "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" + "test-bacteria_odb12-busco.batch_summary.txt:md5,44d4cdebd61a3c8e8981ddf1829f83b3", + "full_table.tsv:md5,696bae3f377fd5dbaf19f1c522088d93", + "missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50", + "versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-03T13:27:12.724862" + "timestamp": "2024-12-11T12:45:16.960592213" } } \ 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 89604dc25c0..5ae259f2a72 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 @@ -46,9 +46,9 @@ ], "12": [ - "versions.yml:md5,36b11c442943567e471af0abd474a10b", + "versions.yml:md5,624e4661a636558db4521457fcddf6dd", "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a", - "versions.yml:md5,e9d65e2f2f13175e99c5b7f4ae1013b9" + "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64" ], "2": [ @@ -172,17 +172,17 @@ ], "versions": [ - "versions.yml:md5,36b11c442943567e471af0abd474a10b", + "versions.yml:md5,624e4661a636558db4521457fcddf6dd", "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a", - "versions.yml:md5,e9d65e2f2f13175e99c5b7f4ae1013b9" + "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64" ] } ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-25T10:31:03.980517" + "timestamp": "2024-12-11T12:47:54.913113837" }, "candidatus_portiera_aleyrodidarum - bacteroides_fragilis - genome": { "content": [ @@ -201,7 +201,7 @@ "mode": "genome", "lineage": "bacteria_odb10" }, - "test-bacteria_odb10-busco.batch_summary.txt:md5,a1186bc25448ac1949bf7790810f7161" + "test-bacteria_odb10-busco.batch_summary.txt:md5,30d9e8403e21e0ac7fa9574a4a7ca825" ], [ { @@ -235,21 +235,21 @@ "mode": "proteins", "lineage": "bacteria_odb10" }, - "test-bacteria_odb10-busco.batch_summary.txt:md5,995127c0caecb36205dbf21aa2f9f8a8" + "test-bacteria_odb10-busco.batch_summary.txt:md5,7b5c7ffb03af12b3854b00d31e2044b0" ] ], [ "versions.yml:md5,05d8022e3afb0d5642ed17147b991730", - "versions.yml:md5,36b11c442943567e471af0abd474a10b", "versions.yml:md5,53987b35fc275297efdaf525937fdca3", + "versions.yml:md5,624e4661a636558db4521457fcddf6dd", "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a", - "versions.yml:md5,e9d65e2f2f13175e99c5b7f4ae1013b9" + "versions.yml:md5,98062b1a1c90be0537d21ccfbf08bc64" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-05-13T16:39:04.376704" + "timestamp": "2024-12-11T12:47:41.989229128" } } \ No newline at end of file