diff --git a/.cache.tar.xz b/.cache.tar.xz index 80b8b2dc8d..deede8d211 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 7d0b35ebca..cadbf1713b 100644 --- a/public/components.json +++ b/public/components.json @@ -8704,6 +8704,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -27987,6 +27991,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -108877,6 +108885,22 @@ "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" @@ -115253,6 +115277,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -122330,9 +122358,9 @@ "input": [ [ { - "db": { + "database": { "type": "directory", - "description": "Directory containing the DB to be indexed\n", + "description": "Directory containing the database to be indexed\n", "pattern": "*" } } @@ -122342,9 +122370,9 @@ { "db_exprofile": [ { - "db": { + "database": { "type": "directory", - "description": "Directory containing the expandable profile DB\n", + "description": "Directory containing the expandable profile database\n", "pattern": "*" } } @@ -122366,7 +122394,8 @@ "@JoseEspinosa" ], "maintainers": [ - "@JoseEspinosa" + "@JoseEspinosa", + "@sateeshperi" ] }, "pipelines": [ @@ -134345,6 +134374,10 @@ "name": "viralrecon", "version": "2.6.0" }, + { + "name": "viralrecon", + "version": "2.6.0" + }, { "name": "viralrecon", "version": "2.6.0" @@ -201793,7 +201826,7 @@ "authors": [ "@pinin4fjords", "@bjlang", - "@araiz2001", + "@caraiz2001", "@suzannejin" ], "maintainers": [ @@ -209531,6 +209564,10 @@ "name": "phageannotator", "version": "dev" }, + { + "name": "phageannotator", + "version": "dev" + }, { "name": "phageannotator", "version": "dev" @@ -213281,6 +213318,10 @@ "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 00984ebfe4..4f44149004 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -566,7 +566,7 @@ "forks_count": 123, "archived": false, "disabled": false, - "open_issues_count": 31, + "open_issues_count": 30, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -589,7 +589,7 @@ ], "visibility": "public", "forks": 123, - "open_issues": 31, + "open_issues": 30, "watchers": 190, "default_branch": "master", "temp_clone_token": "", @@ -4724,10 +4724,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/circrna", "created_at": "2021-02-10T14:28:49Z", - "updated_at": "2024-12-30T09:22:59Z", - "pushed_at": "2024-12-20T13:06:25Z", + "updated_at": "2025-01-16T10:27:28Z", + "pushed_at": "2025-01-16T10:29:06Z", "homepage": "https://nf-co.re/circrna", - "size": 73584, + "size": 73577, "stargazers_count": 48, "watchers_count": 48, "language": "Nextflow", @@ -4865,7 +4865,7 @@ }, { "name": "nictru", - "count": 483, + "count": 485, "avatar_url": "https://avatars.githubusercontent.com/u/52698566?v=4" }, { @@ -4910,9 +4910,9 @@ } ], "released_after_tools": false, - "head_sha": "abdc4cb19b23ebafd2e769ae59e87d51002f61f4", + "head_sha": "bf801f5e8997d246a10b60dc231ab05b7fc6579e", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/circrna/compare/abdc4cb19b23ebafd2e769ae59e87d51002f61f4...undefined", + "last_release_vs_default_compare_url": "https://github.com/nf-core/circrna/compare/bf801f5e8997d246a10b60dc231ab05b7fc6579e...undefined", "commits_to_dev": 30, "is_DSL2": true, "has_nf_test": false, @@ -4930,8 +4930,8 @@ "releases": [ { "tag_name": "dev", - "published_at": "2024-12-16T09:06:44Z", - "tag_sha": "abdc4cb19b23ebafd2e769ae59e87d51002f61f4", + "published_at": "2025-01-16T10:27:19Z", + "tag_sha": "bf801f5e8997d246a10b60dc231ab05b7fc6579e", "has_schema": true, "doc_files": [ "docs/output.md", @@ -10755,7 +10755,7 @@ "forks_count": 41, "archived": false, "disabled": false, - "open_issues_count": 81, + "open_issues_count": 82, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10773,7 +10773,7 @@ ], "visibility": "public", "forks": 41, - "open_issues": 81, + "open_issues": 82, "watchers": 68, "default_branch": "master", "temp_clone_token": "", @@ -11722,7 +11722,7 @@ "forks_count": 82, "archived": false, "disabled": false, - "open_issues_count": 49, + "open_issues_count": 45, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -11737,7 +11737,7 @@ ], "visibility": "public", "forks": 82, - "open_issues": 49, + "open_issues": 45, "watchers": 155, "default_branch": "master", "temp_clone_token": "", @@ -12389,7 +12389,7 @@ "forks_count": 23, "archived": false, "disabled": false, - "open_issues_count": 18, + "open_issues_count": 19, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -12400,7 +12400,7 @@ ], "visibility": "public", "forks": 23, - "open_issues": 18, + "open_issues": 19, "watchers": 43, "default_branch": "master", "temp_clone_token": "", @@ -12488,7 +12488,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 2, + "open_pr_count": 3, "repository_url": "https://github.com/nf-core/epitopeprediction", "contributors": [ { @@ -13103,7 +13103,7 @@ "forks_count": 11, "archived": false, "disabled": false, - "open_issues_count": 15, + "open_issues_count": 16, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -13115,7 +13115,7 @@ ], "visibility": "public", "forks": 11, - "open_issues": 15, + "open_issues": 16, "watchers": 20, "default_branch": "master", "temp_clone_token": "", @@ -13895,9 +13895,9 @@ "url": "https://api.github.com/repos/nf-core/funcscan", "created_at": "2021-12-13T10:35:54Z", "updated_at": "2025-01-06T19:48:18Z", - "pushed_at": "2025-01-15T18:33:34Z", + "pushed_at": "2025-01-16T11:41:40Z", "homepage": "https://nf-co.re/funcscan", - "size": 19163, + "size": 19173, "stargazers_count": 77, "watchers_count": 77, "language": "Nextflow", @@ -13910,7 +13910,7 @@ "forks_count": 22, "archived": false, "disabled": false, - "open_issues_count": 18, + "open_issues_count": 17, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -13933,7 +13933,7 @@ ], "visibility": "public", "forks": 22, - "open_issues": 18, + "open_issues": 17, "watchers": 77, "default_branch": "master", "temp_clone_token": "", @@ -14151,7 +14151,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 2, "repository_url": "https://github.com/nf-core/funcscan", "contributors": [ { @@ -14735,8 +14735,8 @@ }, { "tag_name": "dev", - "published_at": "2025-01-15T13:22:58Z", - "tag_sha": "b89ec1be6cacddb1b36e1c47d08164f183fc9338", + "published_at": "2025-01-16T11:41:39Z", + "tag_sha": "21f79699cb2180dc6c40a78f818eee879021c941", "has_schema": true, "doc_files": [ "docs/output.md", @@ -18902,7 +18902,7 @@ "forks_count": 115, "archived": false, "disabled": false, - "open_issues_count": 73, + "open_issues_count": 74, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -18918,7 +18918,7 @@ ], "visibility": "public", "forks": 115, - "open_issues": 73, + "open_issues": 74, "watchers": 225, "default_branch": "master", "temp_clone_token": "", @@ -21340,10 +21340,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/meerpipe", "created_at": "2023-05-24T00:09:36Z", - "updated_at": "2025-01-07T04:48:00Z", - "pushed_at": "2025-01-07T04:47:57Z", + "updated_at": "2025-01-16T05:12:54Z", + "pushed_at": "2025-01-16T05:12:52Z", "homepage": "", - "size": 2890, + "size": 2894, "stargazers_count": 7, "watchers_count": 7, "language": "Nextflow", @@ -21356,14 +21356,14 @@ "forks_count": 4, "archived": false, "disabled": false, - "open_issues_count": 2, + "open_issues_count": 1, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 4, - "open_issues": 2, + "open_issues": 1, "watchers": 7, "default_branch": "dev", "temp_clone_token": "", @@ -21443,7 +21443,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": false, - "open_pr_count": 2, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/meerpipe", "contributors": [ { @@ -21453,14 +21453,14 @@ }, { "name": "emmacarli", - "count": 3, + "count": 8, "avatar_url": "https://avatars.githubusercontent.com/u/39613453?v=4" } ], "released_after_tools": false, - "head_sha": "112802e2497ab3a2222f8d83da2447e505ccffe4", + "head_sha": "aeb6989907d933b78de91c9ce24a4854be6e1f05", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/meerpipe/compare/112802e2497ab3a2222f8d83da2447e505ccffe4...undefined", + "last_release_vs_default_compare_url": "https://github.com/nf-core/meerpipe/compare/aeb6989907d933b78de91c9ce24a4854be6e1f05...undefined", "commits_to_dev": 30, "is_DSL2": true, "has_nf_test": true, @@ -21481,8 +21481,8 @@ "releases": [ { "tag_name": "dev", - "published_at": "2025-01-07T04:47:55Z", - "tag_sha": "112802e2497ab3a2222f8d83da2447e505ccffe4", + "published_at": "2025-01-16T05:12:51Z", + "tag_sha": "aeb6989907d933b78de91c9ce24a4854be6e1f05", "has_schema": true, "doc_files": [ "docs/output.md", @@ -22478,12 +22478,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/methylseq", "created_at": "2018-03-12T15:46:42Z", - "updated_at": "2025-01-06T12:04:10Z", + "updated_at": "2025-01-16T09:06:57Z", "pushed_at": "2024-12-23T11:23:08Z", "homepage": "https://nf-co.re/methylseq", "size": 24700, - "stargazers_count": 153, - "watchers_count": 153, + "stargazers_count": 154, + "watchers_count": 154, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -22511,7 +22511,7 @@ "visibility": "public", "forks": 146, "open_issues": 26, - "watchers": 153, + "watchers": 154, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -26469,12 +26469,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/pacvar", "created_at": "2024-09-17T21:39:08Z", - "updated_at": "2025-01-11T10:40:57Z", + "updated_at": "2025-01-16T10:13:55Z", "pushed_at": "2024-12-30T23:52:13Z", "homepage": "https://nf-co.re/pacvar", "size": 356499, - "stargazers_count": 2, - "watchers_count": 2, + "stargazers_count": 3, + "watchers_count": 3, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -26500,7 +26500,7 @@ "visibility": "public", "forks": 2, "open_issues": 5, - "watchers": 2, + "watchers": 3, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -26949,9 +26949,9 @@ "url": "https://api.github.com/repos/nf-core/pangenome", "created_at": "2020-11-08T18:02:43Z", "updated_at": "2025-01-14T01:17:58Z", - "pushed_at": "2025-01-15T16:24:14Z", + "pushed_at": "2025-01-16T08:42:30Z", "homepage": "https://nf-co.re/pangenome", - "size": 4333, + "size": 4335, "stargazers_count": 80, "watchers_count": 80, "language": "Nextflow", @@ -26964,7 +26964,7 @@ "forks_count": 18, "archived": false, "disabled": false, - "open_issues_count": 15, + "open_issues_count": 12, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -26973,7 +26973,7 @@ ], "visibility": "public", "forks": 18, - "open_issues": 15, + "open_issues": 12, "watchers": 80, "default_branch": "master", "temp_clone_token": "", @@ -27076,7 +27076,7 @@ "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/pangenome", "contributors": [ { @@ -27292,8 +27292,8 @@ }, { "tag_name": "dev", - "published_at": "2025-01-15T16:24:14Z", - "tag_sha": "5a5941c9610d2087c064d0d8d4e9f1232f5b1c7d", + "published_at": "2025-01-16T08:42:30Z", + "tag_sha": "10beeb41725965d02b4343b29495bde709c890f5", "has_schema": true, "doc_files": [ "docs/output.md", @@ -28833,9 +28833,9 @@ "url": "https://api.github.com/repos/nf-core/pixelator", "created_at": "2022-09-17T18:27:29Z", "updated_at": "2024-09-03T10:12:04Z", - "pushed_at": "2025-01-15T16:05:36Z", + "pushed_at": "2025-01-16T11:23:55Z", "homepage": "https://nf-co.re/pixelator", - "size": 4767, + "size": 4773, "stargazers_count": 8, "watchers_count": 8, "language": "Nextflow", @@ -29150,8 +29150,8 @@ }, { "tag_name": "dev", - "published_at": "2025-01-15T16:05:25Z", - "tag_sha": "034ef888f9d21aee792c59dd3858556303c529f5", + "published_at": "2025-01-16T11:23:49Z", + "tag_sha": "47af4cbf296fa630debcdc391b6ae5d906c1174d", "has_schema": true, "doc_files": [ "docs/output.md", @@ -30088,7 +30088,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 71, + "open_issues_count": 72, "license": { "key": "mit", "name": "MIT License", @@ -30108,7 +30108,7 @@ ], "visibility": "public", "forks": 38, - "open_issues": 71, + "open_issues": 72, "watchers": 34, "default_branch": "master" }, @@ -30201,7 +30201,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 71, + "open_issues_count": 72, "license": { "key": "mit", "name": "MIT License", @@ -30221,7 +30221,7 @@ ], "visibility": "public", "forks": 38, - "open_issues": 71, + "open_issues": 72, "watchers": 34, "default_branch": "master" }, @@ -30883,9 +30883,9 @@ "url": "https://api.github.com/repos/nf-core/raredisease", "created_at": "2021-06-21T09:40:29Z", "updated_at": "2025-01-11T10:36:52Z", - "pushed_at": "2025-01-15T17:59:55Z", + "pushed_at": "2025-01-16T08:17:06Z", "homepage": "https://nf-co.re/raredisease", - "size": 13711, + "size": 13765, "stargazers_count": 93, "watchers_count": 93, "language": "Nextflow", @@ -30898,7 +30898,7 @@ "forks_count": 37, "archived": false, "disabled": false, - "open_issues_count": 37, + "open_issues_count": 36, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -30914,7 +30914,7 @@ ], "visibility": "public", "forks": 37, - "open_issues": 37, + "open_issues": 36, "watchers": 93, "default_branch": "master", "temp_clone_token": "", @@ -31042,7 +31042,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 2, "repository_url": "https://github.com/nf-core/raredisease", "contributors": [ { @@ -31935,8 +31935,8 @@ }, { "tag_name": "dev", - "published_at": "2025-01-15T11:53:19Z", - "tag_sha": "2cf56eea68fdb2b35acf30735d4c6e31ae80838a", + "published_at": "2025-01-16T08:17:00Z", + "tag_sha": "dd764c02bbb5e6378d1ae87c8bf78aa6c993bf14", "has_schema": true, "doc_files": [ "docs/output.md", @@ -34205,12 +34205,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", - "updated_at": "2025-01-15T09:25:21Z", + "updated_at": "2025-01-16T12:43:44Z", "pushed_at": "2025-01-13T11:08:36Z", "homepage": "https://nf-co.re/rnaseq", "size": 74980, - "stargazers_count": 958, - "watchers_count": 958, + "stargazers_count": 960, + "watchers_count": 960, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -34218,10 +34218,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 717, + "forks_count": 716, "archived": false, "disabled": false, - "open_issues_count": 78, + "open_issues_count": 76, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -34230,9 +34230,9 @@ "rna-seq" ], "visibility": "public", - "forks": 717, - "open_issues": 78, - "watchers": 958, + "forks": 716, + "open_issues": 76, + "watchers": 960, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -34266,7 +34266,7 @@ "status": "disabled" } }, - "network_count": 717, + "network_count": 716, "subscribers_count": 158, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -44695,14 +44695,14 @@ "forks_count": 1, "archived": false, "disabled": false, - "open_issues_count": 1, + "open_issues_count": 0, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 1, - "open_issues": 1, + "open_issues": 0, "watchers": 2, "default_branch": "dev", "temp_clone_token": "", @@ -44766,7 +44766,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": -1, "has_required_topics": false, - "open_pr_count": 1, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/stableexpression", "contributors": [ {