diff --git a/.cache.tar.xz b/.cache.tar.xz index f14d96f70d..2dcb0c60c6 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 7a7e9f34d1..714257c730 100644 --- a/public/components.json +++ b/public/components.json @@ -8553,6 +8553,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -13947,6 +13951,123 @@ } ] }, + { + "name": "bbmap_repair", + "path": "modules/nf-core/bbmap/repair/meta.yml", + "type": "module", + "meta": { + "name": "bbmap_repair", + "description": "Re-pairs reads that became disordered or had some mates eliminated.", + "keywords": [ + "paired reads re-pairing", + "fastq", + "preprocessing" + ], + "tools": [ + { + "repair": { + "description": "Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.", + "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/", + "documentation": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/", + "licence": [ + "UC-LBL license (see package)" + ], + "identifier": "biotools:bbmap" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "reads": { + "type": "file", + "description": "List of input paired end fastq files\n", + "pattern": "*.{fastq,fq}.gz" + } + } + ], + [ + { + "interleave": { + "type": "boolean", + "description": "Indicates whether the input paired reads are interleaved or not\n" + } + } + ] + ], + "output": [ + { + "repaired": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "*_repaired.fastq.gz": { + "type": "file", + "description": "re-paired reads", + "pattern": "*_repaired.fastq.gz" + } + } + ] + }, + { + "singleton": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "${prefix}_singleton.fastq.gz": { + "type": "file", + "description": "singleton reads", + "pattern": "*singleton.fastq.gz" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + }, + { + "log": [ + { + "*.log": { + "type": "file", + "description": "log file containing stdout and stderr from repair.sh", + "pattern": "*.log" + } + } + ] + } + ], + "authors": [ + "@mazzalab" + ], + "maintainers": [ + "@mazzalab", + "@tm4zza" + ] + } + }, { "name": "bbmap_sendsketch", "path": "modules/nf-core/bbmap/sendsketch/meta.yml", @@ -27633,6 +27754,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -86499,7 +86624,7 @@ { "fastqgz": { "type": "file", - "description": "FASTQ.gz file", + "description": "FASTQ.gz files", "pattern": "*.{gz}", "ontologies": [ { @@ -86512,7 +86637,7 @@ ], "output": [ { - "fastqrecovered": [ + "recovered": [ { "meta": { "type": "map", @@ -86520,9 +86645,9 @@ } }, { - "*_recovered.fastq.gz": { + "${prefix}*.fastq.gz": { "type": "file", - "description": "Recovered FASTQ.gz file", + "description": "Recovered FASTQ.gz files", "pattern": "*.{gz}", "ontologies": [ { @@ -107965,6 +108090,22 @@ "name": "pathogensurveillance", "version": "dev" }, + { + "name": "phyloplace", + "version": "1.0.0" + }, + { + "name": "ampliseq", + "version": "2.12.0" + }, + { + "name": "multiplesequencealign", + "version": "1.0.0" + }, + { + "name": "pathogensurveillance", + "version": "dev" + }, { "name": "phyloplace", "version": "1.0.0" @@ -114267,6 +114408,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -133259,6 +133404,10 @@ "name": "viralrecon", "version": "2.6.0" }, + { + "name": "viralrecon", + "version": "2.6.0" + }, { "name": "viralrecon", "version": "2.6.0" @@ -207857,6 +208006,10 @@ "name": "phageannotator", "version": "dev" }, + { + "name": "phageannotator", + "version": "dev" + }, { "name": "phageannotator", "version": "dev" @@ -211539,6 +211692,10 @@ "name": "riboseq", "version": "1.0.1" }, + { + "name": "riboseq", + "version": "1.0.1" + }, { "name": "riboseq", "version": "1.0.1" diff --git a/public/pipelines.json b/public/pipelines.json index 6c47f30324..aa4d5a4387 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -10724,9 +10724,9 @@ "url": "https://api.github.com/repos/nf-core/differentialabundance", "created_at": "2022-10-12T08:49:25Z", "updated_at": "2025-01-03T21:35:31Z", - "pushed_at": "2024-12-31T21:47:07Z", + "pushed_at": "2025-01-07T19:10:22Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 9265, + "size": 9320, "stargazers_count": 67, "watchers_count": 67, "language": "Nextflow", @@ -10739,7 +10739,7 @@ "forks_count": 41, "archived": false, "disabled": false, - "open_issues_count": 84, + "open_issues_count": 83, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10757,7 +10757,7 @@ ], "visibility": "public", "forks": 41, - "open_issues": 84, + "open_issues": 83, "watchers": 67, "default_branch": "master", "temp_clone_token": "", @@ -10855,7 +10855,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 10, + "open_pr_count": 9, "repository_url": "https://github.com/nf-core/differentialabundance", "contributors": [ { @@ -15189,12 +15189,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/genomeqc", "created_at": "2024-09-25T13:21:38Z", - "updated_at": "2024-12-10T14:10:30Z", + "updated_at": "2025-01-07T19:55:47Z", "pushed_at": "2024-12-20T13:08:27Z", "homepage": "https://nf-co.re/genomeqc", "size": 602, - "stargazers_count": 4, - "watchers_count": 4, + "stargazers_count": 5, + "watchers_count": 5, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -15218,7 +15218,7 @@ "visibility": "public", "forks": 11, "open_issues": 42, - "watchers": 4, + "watchers": 5, "default_branch": "dev", "temp_clone_token": "", "allow_squash_merge": true, @@ -17801,7 +17801,7 @@ } }, "network_count": 13, - "subscribers_count": 142, + "subscribers_count": 141, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -27281,13 +27281,13 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/pathogensurveillance", "created_at": "2023-01-12T17:57:12Z", - "updated_at": "2024-12-17T18:58:40Z", - "pushed_at": "2024-12-20T16:00:26Z", + "updated_at": "2025-01-07T18:52:33Z", + "pushed_at": "2025-01-07T18:52:22Z", "homepage": "https://nf-co.re/pathogensurveillance", - "size": 272488, + "size": 273541, "stargazers_count": 14, "watchers_count": 14, - "language": "HTML", + "language": "Nextflow", "has_issues": true, "has_projects": false, "has_downloads": true, @@ -27297,14 +27297,14 @@ "forks_count": 6, "archived": false, "disabled": false, - "open_issues_count": 43, + "open_issues_count": 42, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 6, - "open_issues": 43, + "open_issues": 42, "watchers": 14, "default_branch": "dev", "temp_clone_token": "", @@ -27394,7 +27394,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 1, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/pathogensurveillance", "contributors": [ { @@ -27404,12 +27404,12 @@ }, { "name": "grunwald", - "count": 65, + "count": 69, "avatar_url": "https://avatars.githubusercontent.com/u/3679546?v=4" }, { "name": "cahuparo", - "count": 54, + "count": 55, "avatar_url": "https://avatars.githubusercontent.com/u/28018971?v=4" }, { @@ -27449,13 +27449,13 @@ } ], "released_after_tools": false, - "head_sha": "ee2764e6537941fdb83ea1210974bf75937cfde0", + "head_sha": "87e6e39b57245277409790758d10fca407d86a2e", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/pathogensurveillance/compare/ee2764e6537941fdb83ea1210974bf75937cfde0...undefined", + "last_release_vs_default_compare_url": "https://github.com/nf-core/pathogensurveillance/compare/87e6e39b57245277409790758d10fca407d86a2e...undefined", "commits_to_dev": 30, "is_DSL2": true, - "has_nf_test": false, - "has_nf_test_dev": false, + "has_nf_test": true, + "has_nf_test_dev": true, "master_nextflow_config_plugins": null, "master_nextflow_config_manifest": { "defaultBranch": null @@ -27465,15 +27465,15 @@ ], "dev_nextflow_config_manifest": { "defaultBranch": [ - "defaultBranch = 'master'", - "master" + "defaultBranch = 'main'", + "main" ] }, "releases": [ { "tag_name": "dev", - "published_at": "2024-12-17T18:58:23Z", - "tag_sha": "ee2764e6537941fdb83ea1210974bf75937cfde0", + "published_at": "2025-01-07T18:50:37Z", + "tag_sha": "87e6e39b57245277409790758d10fca407d86a2e", "has_schema": true, "doc_files": [ "docs/output.md", @@ -29119,12 +29119,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/proteinfold", "created_at": "2022-03-03T10:41:35Z", - "updated_at": "2024-12-16T08:08:13Z", + "updated_at": "2025-01-07T17:15:24Z", "pushed_at": "2024-12-20T13:10:06Z", "homepage": "https://nf-co.re/proteinfold", "size": 6785, - "stargazers_count": 64, - "watchers_count": 64, + "stargazers_count": 65, + "watchers_count": 65, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -29135,7 +29135,7 @@ "forks_count": 43, "archived": false, "disabled": false, - "open_issues_count": 36, + "open_issues_count": 37, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -29148,8 +29148,8 @@ ], "visibility": "public", "forks": 43, - "open_issues": 36, - "watchers": 64, + "open_issues": 37, + "watchers": 65, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -29241,7 +29241,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 6, + "open_pr_count": 7, "repository_url": "https://github.com/nf-core/proteinfold", "contributors": [ { @@ -30630,9 +30630,9 @@ "url": "https://api.github.com/repos/nf-core/raredisease", "created_at": "2021-06-21T09:40:29Z", "updated_at": "2024-12-30T16:56:18Z", - "pushed_at": "2025-01-07T10:42:18Z", + "pushed_at": "2025-01-07T15:26:06Z", "homepage": "https://nf-co.re/raredisease", - "size": 13634, + "size": 13635, "stargazers_count": 92, "watchers_count": 92, "language": "Nextflow", @@ -30645,7 +30645,7 @@ "forks_count": 37, "archived": false, "disabled": false, - "open_issues_count": 37, + "open_issues_count": 38, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -30661,7 +30661,7 @@ ], "visibility": "public", "forks": 37, - "open_issues": 37, + "open_issues": 38, "watchers": 92, "default_branch": "master", "temp_clone_token": "", @@ -30789,7 +30789,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 4, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/raredisease", "contributors": [ { @@ -32059,7 +32059,7 @@ "updated_at": "2024-10-21T17:45:17Z", "pushed_at": "2025-01-07T14:58:16Z", "homepage": "", - "size": 2098, + "size": 2105, "stargazers_count": 9, "watchers_count": 9, "language": "Nextflow", @@ -32938,9 +32938,9 @@ "url": "https://api.github.com/repos/nf-core/rnafusion", "created_at": "2018-10-05T13:05:57Z", "updated_at": "2024-12-26T15:27:43Z", - "pushed_at": "2025-01-07T12:56:53Z", + "pushed_at": "2025-01-07T17:22:10Z", "homepage": "https://nf-co.re/rnafusion", - "size": 20109, + "size": 20072, "stargazers_count": 148, "watchers_count": 148, "language": "Nextflow", @@ -32950,7 +32950,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - 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"updated_at": "2024-12-31T22:27:12Z", + "updated_at": "2025-01-08T02:11:03Z", "pushed_at": "2024-12-20T13:13:11Z", "homepage": "https://nf-co.re/sarek", "size": 98869, - "stargazers_count": 414, - "watchers_count": 414, + "stargazers_count": 413, + "watchers_count": 413, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -37168,7 +37168,7 @@ "visibility": "public", "forks": 417, "open_issues": 299, - "watchers": 414, + "watchers": 413, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -39850,7 +39850,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 14, + "forks_count": 15, "archived": false, "disabled": false, "open_issues_count": 29, @@ -39866,7 +39866,7 @@ "single-cell" ], "visibility": "public", - "forks": 14, + "forks": 15, "open_issues": 29, "watchers": 44, "default_branch": "dev", @@ -39900,7 +39900,7 @@ "status": "disabled" } }, - "network_count": 14, + "network_count": 15, "subscribers_count": 179, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -40505,9 +40505,9 @@ "url": "https://api.github.com/repos/nf-core/scnanoseq", "created_at": "2022-04-08T15:41:14Z", "updated_at": "2025-01-06T11:39:40Z", - "pushed_at": "2024-12-24T03:56:10Z", + "pushed_at": "2025-01-07T22:01:31Z", "homepage": "https://nf-co.re/scnanoseq/", - "size": 24230, + "size": 24242, "stargazers_count": 22, "watchers_count": 22, "language": "Nextflow", @@ -40717,8 +40717,8 @@ }, { "tag_name": "dev", - "published_at": "2024-12-24T03:56:10Z", - "tag_sha": "5c964ec176426ca0dba75d17f294fbbb52dcdcc8", + "published_at": "2025-01-07T22:01:09Z", + "tag_sha": "fd584dd93c8968087cebb26c9014717d8f0e8cfc", "has_schema": true, "doc_files": [ "docs/output.md", @@ -42668,9 +42668,9 @@ "url": "https://api.github.com/repos/nf-core/smrnaseq", "created_at": "2018-07-11T14:56:59Z", "updated_at": "2024-12-23T13:13:54Z", - "pushed_at": "2024-12-26T18:11:25Z", + "pushed_at": "2025-01-07T19:42:09Z", "homepage": "https://nf-co.re/smrnaseq", - "size": 8870, + "size": 8879, "stargazers_count": 76, "watchers_count": 76, "language": "Nextflow", @@ -42683,7 +42683,7 @@ "forks_count": 127, "archived": false, "disabled": false, - "open_issues_count": 12, + "open_issues_count": 13, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -42693,7 +42693,7 @@ ], "visibility": "public", "forks": 127, - "open_issues": 12, + "open_issues": 13, "watchers": 76, "default_branch": "master", "temp_clone_token": "", @@ -42781,7 +42781,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 1, + "open_pr_count": 2, "repository_url": "https://github.com/nf-core/smrnaseq", "contributors": [ { @@ -43373,12 +43373,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/spatialvi", "created_at": "2022-02-23T20:44:38Z", - "updated_at": "2024-12-25T00:57:52Z", + "updated_at": "2025-01-07T15:10:16Z", "pushed_at": "2024-12-20T13:53:38Z", "homepage": "https://nf-co.re/spatialvi", "size": 7361, - "stargazers_count": 52, - "watchers_count": 52, + "stargazers_count": 53, + "watchers_count": 53, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -43409,7 +43409,7 @@ "visibility": "public", "forks": 20, "open_issues": 8, - "watchers": 52, + "watchers": 53, "default_branch": "dev", "temp_clone_token": "", "allow_squash_merge": false, @@ -43595,12 +43595,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/spatialxe", "created_at": "2024-03-14T10:57:36Z", - "updated_at": "2025-01-05T16:40:40Z", + "updated_at": "2025-01-07T15:06:13Z", "pushed_at": "2024-12-20T13:13:14Z", "homepage": "https://nf-co.re/spatialxe", "size": 7483, - "stargazers_count": 6, - "watchers_count": 6, + "stargazers_count": 7, + "watchers_count": 7, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -43619,7 +43619,7 @@ "visibility": "public", "forks": 3, "open_issues": 31, - "watchers": 6, + "watchers": 7, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -43652,7 +43652,7 @@ } }, "network_count": 3, - "subscribers_count": 190, + "subscribers_count": 189, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -46120,7 +46120,7 @@ } }, "network_count": 1, - "subscribers_count": 197, + "subscribers_count": 196, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -46231,12 +46231,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/tumourevo", "created_at": "2024-02-02T17:16:47Z", - "updated_at": "2025-01-07T11:28:30Z", + "updated_at": "2025-01-07T21:37:17Z", "pushed_at": "2024-12-20T14:21:07Z", "homepage": "https://nf-co.re/tumourevo", "size": 2645, - "stargazers_count": 9, - "watchers_count": 9, + "stargazers_count": 10, + "watchers_count": 10, "language": null, "has_issues": true, "has_projects": false, @@ -46264,7 +46264,7 @@ "visibility": "public", "forks": 4, "open_issues": 4, - "watchers": 9, + "watchers": 10, "default_branch": "main", "temp_clone_token": "", "allow_squash_merge": false, @@ -47320,9 +47320,9 @@ "url": "https://api.github.com/repos/nf-core/viralrecon", "created_at": "2020-03-30T11:14:12Z", "updated_at": "2024-12-16T14:09:19Z", - "pushed_at": "2025-01-06T15:41:01Z", + "pushed_at": "2025-01-07T22:07:22Z", "homepage": "https://nf-co.re/viralrecon", - "size": 10393, + "size": 10390, "stargazers_count": 128, "watchers_count": 128, "language": "Nextflow", @@ -47335,7 +47335,7 @@ "forks_count": 114, "archived": false, "disabled": false, - "open_issues_count": 38, + "open_issues_count": 37, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -47358,7 +47358,7 @@ ], "visibility": "public", "forks": 114, - "open_issues": 38, + "open_issues": 37, "watchers": 128, "default_branch": "master", "temp_clone_token": "", @@ -47456,7 +47456,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 4, + "open_pr_count": 3, "repository_url": "https://github.com/nf-core/viralrecon", "contributors": [ {