diff --git a/.cache.tar.xz b/.cache.tar.xz index cb07fca03f..35b1b1ac4d 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 9c219d7976..a6731fee9a 100644 --- a/public/components.json +++ b/public/components.json @@ -8393,6 +8393,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -27285,6 +27289,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -106596,6 +106608,22 @@ "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" @@ -112758,6 +112786,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -204891,6 +204923,10 @@ "name": "phageannotator", "version": "dev" }, + { + "name": "phageannotator", + "version": "dev" + }, { "name": "phageannotator", "version": "dev" @@ -208433,6 +208469,10 @@ "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 ec83af50c8..478d2b79c9 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -1537,7 +1537,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 118, + "forks_count": 119, "archived": false, "disabled": false, "open_issues_count": 36, @@ -1549,7 +1549,7 @@ "chromatin-accessibiity" ], "visibility": "public", - "forks": 118, + "forks": 119, "open_issues": 36, "watchers": 192, "default_branch": "master", @@ -1583,7 +1583,7 @@ "status": "disabled" } }, - "network_count": 118, + "network_count": 119, "subscribers_count": 149, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -3870,9 +3870,9 @@ "url": "https://api.github.com/repos/nf-core/chipseq", "created_at": "2018-04-24T15:42:59Z", "updated_at": "2024-12-05T17:50:12Z", - "pushed_at": "2024-11-27T17:24:08Z", + "pushed_at": "2024-12-09T15:57:50Z", "homepage": "https://nf-co.re/chipseq", - "size": 16632, + "size": 16634, "stargazers_count": 198, "watchers_count": 198, "language": "Nextflow", @@ -3885,7 +3885,7 @@ "forks_count": 150, "archived": false, "disabled": false, - "open_issues_count": 17, + "open_issues_count": 18, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -3898,7 +3898,7 @@ ], "visibility": "public", "forks": 150, - "open_issues": 17, + "open_issues": 18, "watchers": 198, "default_branch": "master", "temp_clone_token": "", @@ -3986,7 +3986,7 @@ "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/chipseq", "contributors": [ { @@ -6087,9 +6087,9 @@ "url": "https://api.github.com/repos/nf-core/crisprseq", "created_at": "2022-07-14T11:14:34Z", "updated_at": "2024-12-03T15:42:53Z", - "pushed_at": "2024-11-11T08:04:19Z", + "pushed_at": "2024-12-09T14:35:02Z", "homepage": "https://nf-co.re/crisprseq", - "size": 19259, + "size": 19275, "stargazers_count": 34, "watchers_count": 34, "language": "Nextflow", @@ -6102,7 +6102,7 @@ "forks_count": 26, "archived": false, "disabled": false, - "open_issues_count": 24, + "open_issues_count": 25, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -6114,7 +6114,7 @@ ], "visibility": "public", "forks": 26, - "open_issues": 24, + "open_issues": 25, "watchers": 34, "default_branch": "master", "temp_clone_token": "", @@ -6188,7 +6188,7 @@ "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/crisprseq", "contributors": [ { @@ -11021,9 +11021,9 @@ "url": "https://api.github.com/repos/nf-core/differentialabundance", "created_at": "2022-10-12T08:49:25Z", "updated_at": "2024-12-05T19:05:56Z", - "pushed_at": "2024-12-07T00:12:29Z", + "pushed_at": "2024-12-09T14:08:25Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 9121, + "size": 9124, "stargazers_count": 66, "watchers_count": 66, "language": "Nextflow", @@ -11036,7 +11036,7 @@ "forks_count": 37, "archived": false, "disabled": false, - "open_issues_count": 63, + "open_issues_count": 64, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -11054,7 +11054,7 @@ ], "visibility": "public", "forks": 37, - "open_issues": 63, + "open_issues": 64, "watchers": 66, "default_branch": "master", "temp_clone_token": "", @@ -11152,7 +11152,7 @@ "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/differentialabundance", "contributors": [ { @@ -13763,12 +13763,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/fetchngs", "created_at": "2021-06-03T09:26:41Z", - "updated_at": "2024-11-21T10:33:20Z", + "updated_at": "2024-12-09T16:25:09Z", "pushed_at": "2024-12-06T00:38:09Z", "homepage": "https://nf-co.re/fetchngs", "size": 4175, - "stargazers_count": 151, - "watchers_count": 151, + "stargazers_count": 152, + "watchers_count": 152, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -13795,7 +13795,7 @@ "visibility": "public", "forks": 73, "open_issues": 30, - "watchers": 151, + "watchers": 152, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -14306,9 +14306,9 @@ "url": "https://api.github.com/repos/nf-core/funcscan", "created_at": "2021-12-13T10:35:54Z", "updated_at": "2024-10-31T15:49:14Z", - "pushed_at": "2024-12-09T07:19:13Z", + "pushed_at": "2024-12-09T15:23:10Z", "homepage": "https://nf-co.re/funcscan", - "size": 18598, + "size": 18610, "stargazers_count": 74, "watchers_count": 74, "language": "Nextflow", @@ -14321,7 +14321,7 @@ "forks_count": 20, "archived": false, "disabled": false, - "open_issues_count": 19, + "open_issues_count": 20, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -14344,7 +14344,7 @@ ], "visibility": "public", "forks": 20, - "open_issues": 19, + "open_issues": 20, "watchers": 74, "default_branch": "master", "temp_clone_token": "", @@ -14562,7 +14562,7 @@ "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/funcscan", "contributors": [ { @@ -15668,9 +15668,9 @@ "url": "https://api.github.com/repos/nf-core/genomeqc", "created_at": "2024-09-25T13:21:38Z", "updated_at": "2024-12-05T17:52:19Z", - "pushed_at": "2024-12-06T11:57:36Z", + "pushed_at": "2024-12-09T18:01:42Z", "homepage": "https://nf-co.re/genomeqc", - "size": 424, + "size": 426, "stargazers_count": 4, "watchers_count": 4, "language": "Nextflow", @@ -15683,7 +15683,7 @@ "forks_count": 10, "archived": false, "disabled": false, - "open_issues_count": 39, + "open_issues_count": 41, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -15695,7 +15695,7 @@ ], "visibility": "public", "forks": 10, - "open_issues": 39, + "open_issues": 41, "watchers": 4, "default_branch": "dev", "temp_clone_token": "", @@ -15759,7 +15759,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": -1, "has_required_topics": false, - "open_pr_count": 4, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/genomeqc", "contributors": [ { @@ -19494,7 +19494,7 @@ "forks_count": 111, "archived": false, "disabled": false, - "open_issues_count": 72, + "open_issues_count": 71, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -19510,7 +19510,7 @@ ], "visibility": "public", "forks": 111, - "open_issues": 72, + "open_issues": 71, "watchers": 218, "default_branch": "master", "temp_clone_token": "", @@ -22088,7 +22088,7 @@ "forks_count": 15, "archived": false, "disabled": false, - "open_issues_count": 3, + "open_issues_count": 4, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -22102,7 +22102,7 @@ ], "visibility": "public", "forks": 15, - "open_issues": 3, + "open_issues": 4, "watchers": 16, "default_branch": "master", "temp_clone_token": "", @@ -22136,7 +22136,7 @@ } }, "network_count": 15, - "subscribers_count": 45, + "subscribers_count": 44, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -23091,9 +23091,9 @@ "url": "https://api.github.com/repos/nf-core/methylseq", "created_at": "2018-03-12T15:46:42Z", "updated_at": "2024-11-30T06:53:00Z", - "pushed_at": "2024-12-05T10:54:05Z", + "pushed_at": "2024-12-09T23:50:56Z", "homepage": "https://nf-co.re/methylseq", - "size": 22726, + "size": 22744, "stargazers_count": 143, "watchers_count": 143, "language": "Nextflow", @@ -23908,7 +23908,7 @@ "forks_count": 25, "archived": false, "disabled": false, - "open_issues_count": 9, + "open_issues_count": 10, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -23922,7 +23922,7 @@ ], "visibility": "public", "forks": 25, - "open_issues": 9, + "open_issues": 10, "watchers": 33, "default_branch": "master", "temp_clone_token": "", @@ -29940,7 +29940,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 40, + "forks_count": 42, "archived": false, "disabled": false, "open_issues_count": 34, @@ -29955,7 +29955,7 @@ "protein-structure" ], "visibility": "public", - "forks": 40, + "forks": 42, "open_issues": 34, "watchers": 62, "default_branch": "master", @@ -29989,7 +29989,7 @@ "status": "disabled" } }, - "network_count": 40, + "network_count": 42, "subscribers_count": 163, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -33871,9 +33871,9 @@ "url": "https://api.github.com/repos/nf-core/rnafusion", "created_at": "2018-10-05T13:05:57Z", "updated_at": "2024-11-30T13:04:24Z", - "pushed_at": "2024-12-09T13:46:58Z", + "pushed_at": "2024-12-09T14:42:11Z", "homepage": "https://nf-co.re/rnafusion", - "size": 19783, + "size": 19788, "stargazers_count": 145, "watchers_count": 145, "language": "Nextflow", @@ -34638,9 +34638,9 @@ "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", "updated_at": "2024-12-09T02:15:42Z", - "pushed_at": "2024-12-06T00:07:44Z", + "pushed_at": "2024-12-09T16:57:11Z", "homepage": "https://nf-co.re/rnaseq", - "size": 74558, + "size": 74559, "stargazers_count": 935, "watchers_count": 935, "language": "Nextflow", @@ -34650,10 +34650,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 708, + "forks_count": 709, "archived": false, "disabled": false, - "open_issues_count": 78, + "open_issues_count": 77, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -34662,8 +34662,8 @@ "rna-seq" ], "visibility": "public", - "forks": 708, - "open_issues": 78, + "forks": 709, + "open_issues": 77, "watchers": 935, "default_branch": "master", "temp_clone_token": "", @@ -34698,7 +34698,7 @@ "status": "disabled" } }, - "network_count": 708, + "network_count": 709, "subscribers_count": 157, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -34768,7 +34768,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 13, + "open_pr_count": 12, "repository_url": "https://github.com/nf-core/rnaseq", "contributors": [ { @@ -36877,8 +36877,8 @@ }, { "tag_name": "dev", - "published_at": "2024-12-04T14:30:21Z", - "tag_sha": "2986385a7d4065ea454d339718606ac42c7cbe96", + "published_at": "2024-12-09T16:57:11Z", + "tag_sha": "674645ea6f31841ed0ee7053973714a666b07455", "has_schema": true, "doc_files": [ "docs/output.md", @@ -38028,9 +38028,9 @@ "url": "https://api.github.com/repos/nf-core/sarek", "created_at": "2019-04-30T15:43:00Z", "updated_at": "2024-12-05T17:51:02Z", - "pushed_at": "2024-12-09T11:04:14Z", + "pushed_at": "2024-12-09T16:06:14Z", "homepage": "https://nf-co.re/sarek", - "size": 95738, + "size": 95622, "stargazers_count": 410, "watchers_count": 410, "language": "Nextflow", @@ -40444,8 +40444,8 @@ }, { "tag_name": "dev", - "published_at": "2024-12-09T10:24:14Z", - "tag_sha": "9569c9386fb1d6899f495743046b80702ab9a625", + "published_at": "2024-12-09T15:49:42Z", + "tag_sha": "2a08c72321b55a25fee267239f31c15d2a640c31", "has_schema": true, "doc_files": [ "docs/output.md", @@ -40582,7 +40582,7 @@ "updated_at": "2024-12-09T13:29:59Z", "pushed_at": "2024-12-09T13:29:58Z", "homepage": "https://nf-co.re/scdownstream", - "size": 1917, + "size": 1918, "stargazers_count": 44, "watchers_count": 44, "language": "Nextflow", @@ -43451,7 +43451,7 @@ "forks_count": 126, "archived": false, "disabled": false, - "open_issues_count": 11, + "open_issues_count": 12, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -43461,7 +43461,7 @@ ], "visibility": "public", "forks": 126, - "open_issues": 11, + "open_issues": 12, "watchers": 74, "default_branch": "master", "temp_clone_token": "", @@ -43549,7 +43549,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 0, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/smrnaseq", "contributors": [ { @@ -44171,7 +44171,7 @@ "forks_count": 19, "archived": false, "disabled": false, - "open_issues_count": 6, + "open_issues_count": 7, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -44190,7 +44190,7 @@ ], "visibility": "public", "forks": 19, - "open_issues": 6, + "open_issues": 7, "watchers": 51, "default_branch": "dev", "temp_clone_token": "", @@ -46973,9 +46973,9 @@ "url": "https://api.github.com/repos/nf-core/tumourevo", "created_at": "2024-02-02T17:16:47Z", "updated_at": "2024-12-05T15:51:37Z", - "pushed_at": "2024-12-06T16:49:00Z", + "pushed_at": "2024-12-09T15:18:30Z", "homepage": "https://nf-co.re/tumourevo", - "size": 5178, + "size": 5184, "stargazers_count": 8, "watchers_count": 8, "language": null, @@ -46988,7 +46988,7 @@ "forks_count": 3, "archived": false, "disabled": false, - "open_issues_count": 5, + "open_issues_count": 4, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -47004,7 +47004,7 @@ ], "visibility": "public", "forks": 3, - "open_issues": 5, + "open_issues": 4, "watchers": 8, "default_branch": "main", "temp_clone_token": "", @@ -47068,7 +47068,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": -1, "has_required_topics": true, - "open_pr_count": 1, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/tumourevo", "contributors": [ { @@ -47110,8 +47110,8 @@ "releases": [ { "tag_name": "dev", - "published_at": "2024-12-06T16:48:59Z", - "tag_sha": "f30b5fb2f7b7a4f47b59a2bfbb000cf2aadbc652", + "published_at": "2024-12-09T15:18:30Z", + "tag_sha": "a8206d5d983e016c3d2dd22dee890fe56ad7d322", "has_schema": true, "doc_files": [ "docs/output.md",