diff --git a/.cache.tar.xz b/.cache.tar.xz index 717e78ce16..957614b207 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 507032200c..050d00db89 100644 --- a/public/components.json +++ b/public/components.json @@ -7800,6 +7800,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -25674,6 +25678,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -107800,6 +107812,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" diff --git a/public/pipelines.json b/public/pipelines.json index 44b78afc7c..7343e7f908 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -26,7 +26,7 @@ "forks_count": 34, "archived": false, "disabled": false, - "open_issues_count": 23, + "open_issues_count": 26, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -39,7 +39,7 @@ ], "visibility": "public", "forks": 34, - "open_issues": 23, + "open_issues": 26, "watchers": 54, "default_branch": "master", "temp_clone_token": "", @@ -2024,7 +2024,7 @@ "forks_count": 41, "archived": false, "disabled": false, - "open_issues_count": 18, + "open_issues_count": 19, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -2040,7 +2040,7 @@ ], "visibility": "public", "forks": 41, - "open_issues": 18, + "open_issues": 19, "watchers": 60, "default_branch": "master", "temp_clone_token": "", @@ -7520,12 +7520,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/deepmodeloptim", "created_at": "2024-03-04T11:37:13Z", - "updated_at": "2024-10-23T13:56:56Z", + "updated_at": "2024-10-23T21:14:54Z", "pushed_at": "2024-10-23T09:08:52Z", "homepage": "https://nf-co.re/deepmodeloptim", "size": 1185, - "stargazers_count": 19, - "watchers_count": 19, + "stargazers_count": 22, + "watchers_count": 22, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -7536,15 +7536,23 @@ "forks_count": 6, "archived": false, "disabled": false, - "open_issues_count": 15, + "open_issues_count": 20, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, - "topics": [], + "topics": [ + "artificial-intelligence", + "dataprocessing", + "deeplearning", + "genomics", + "large-scale", + "optimization", + "prototyping-tool" + ], "visibility": "public", "forks": 6, - "open_issues": 15, - "watchers": 19, + "open_issues": 20, + "watchers": 22, "default_branch": "dev", "temp_clone_token": "", "allow_squash_merge": true, @@ -7577,7 +7585,7 @@ } }, "network_count": 6, - "subscribers_count": 229, + "subscribers_count": 212, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9616,7 +9624,7 @@ "updated_at": "2024-10-21T12:46:07Z", "pushed_at": "2024-10-23T13:08:20Z", "homepage": "https://nf-co.re/detaxizer", - "size": 5521, + "size": 5523, "stargazers_count": 13, "watchers_count": 13, "language": "Nextflow", @@ -10162,7 +10170,7 @@ "updated_at": "2024-10-23T11:13:25Z", "pushed_at": "2024-10-23T13:51:50Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 8584, + "size": 8604, "stargazers_count": 60, "watchers_count": 60, "language": "Nextflow", @@ -10175,7 +10183,7 @@ "forks_count": 33, "archived": false, "disabled": false, - "open_issues_count": 55, + "open_issues_count": 56, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10193,7 +10201,7 @@ ], "visibility": "public", "forks": 33, - "open_issues": 55, + "open_issues": 56, "watchers": 60, "default_branch": "master", "temp_clone_token": "", @@ -10291,7 +10299,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 5, + "open_pr_count": 6, "repository_url": "https://github.com/nf-core/differentialabundance", "contributors": [ { @@ -10766,7 +10774,7 @@ } }, "network_count": 0, - "subscribers_count": 215, + "subscribers_count": 214, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -14219,7 +14227,7 @@ } }, "network_count": 11, - "subscribers_count": 158, + "subscribers_count": 157, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -15060,7 +15068,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 54, + "forks_count": 55, "archived": false, "disabled": false, "open_issues_count": 31, @@ -15072,7 +15080,7 @@ "hi-c" ], "visibility": "public", - "forks": 54, + "forks": 55, "open_issues": 31, "watchers": 90, "default_branch": "master", @@ -15106,7 +15114,7 @@ "status": "disabled" } }, - "network_count": 54, + "network_count": 55, "subscribers_count": 133, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -17780,7 +17788,7 @@ "forks_count": 109, "archived": false, "disabled": false, - "open_issues_count": 65, + "open_issues_count": 67, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -17796,7 +17804,7 @@ ], "visibility": "public", "forks": 109, - "open_issues": 65, + "open_issues": 67, "watchers": 213, "default_branch": "master", "temp_clone_token": "", @@ -21015,7 +21023,7 @@ } }, "network_count": 0, - "subscribers_count": 207, + "subscribers_count": 206, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -21108,9 +21116,9 @@ "url": "https://api.github.com/repos/nf-core/methylseq", "created_at": "2018-03-12T15:46:42Z", "updated_at": "2024-10-19T02:40:02Z", - "pushed_at": "2024-10-23T08:22:35Z", + "pushed_at": "2024-10-23T15:07:56Z", "homepage": "https://nf-co.re/methylseq", - "size": 22401, + "size": 22413, "stargazers_count": 138, "watchers_count": 138, "language": "Nextflow", @@ -21722,8 +21730,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-23T08:22:30Z", - "tag_sha": "d7578f04cbd0c345fc26e219baf8c72316981af7", + "published_at": "2024-10-23T15:07:56Z", + "tag_sha": "0bbf07f9de6d94800d5e0b316a2c0d1c4646a1ca", "has_schema": true, "doc_files": [ "docs/output.md", @@ -23714,7 +23722,7 @@ "updated_at": "2024-09-06T05:39:17Z", "pushed_at": "2024-10-23T13:36:03Z", "homepage": "https://nf-co.re/nascent", - "size": 8772, + "size": 8771, "stargazers_count": 18, "watchers_count": 18, "language": "Nextflow", @@ -25470,10 +25478,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/pathogensurveillance", "created_at": "2023-01-12T17:57:12Z", - "updated_at": "2024-10-22T18:21:40Z", - "pushed_at": "2024-10-23T13:56:24Z", + "updated_at": "2024-10-23T14:07:52Z", + "pushed_at": "2024-10-23T14:08:53Z", "homepage": "https://nf-co.re/pathogensurveillance", - "size": 272023, + "size": 272032, "stargazers_count": 12, "watchers_count": 12, "language": "HTML", @@ -25486,14 +25494,14 @@ "forks_count": 5, "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": 5, - "open_issues": 43, + "open_issues": 42, "watchers": 12, "default_branch": "dev", "temp_clone_token": "", @@ -25527,7 +25535,7 @@ } }, "network_count": 5, - "subscribers_count": 168, + "subscribers_count": 167, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -25583,7 +25591,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 2, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/pathogensurveillance", "contributors": [ { @@ -25621,6 +25629,11 @@ "count": 11, "avatar_url": "https://avatars.githubusercontent.com/u/7210342?v=4" }, + { + "name": "mashehu", + "count": 3, + "avatar_url": "https://avatars.githubusercontent.com/u/6169021?v=4" + }, { "name": "marinawitherell", "count": 3, @@ -25630,17 +25643,12 @@ "name": "phanhung2", "count": 1, "avatar_url": "https://avatars.githubusercontent.com/u/97370288?v=4" - }, - { - "name": "mashehu", - "count": 1, - "avatar_url": "https://avatars.githubusercontent.com/u/6169021?v=4" } ], "released_after_tools": false, - "head_sha": "432a765356a28d883f2bbc54db83d60d82759d68", + "head_sha": "e9be7e38b5242a8840f01830e272e8aaafa784eb", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/pathogensurveillance/compare/432a765356a28d883f2bbc54db83d60d82759d68...undefined", + "last_release_vs_default_compare_url": "https://github.com/nf-core/pathogensurveillance/compare/e9be7e38b5242a8840f01830e272e8aaafa784eb...undefined", "commits_to_dev": 30, "is_DSL2": true, "has_nf_test": false, @@ -25650,8 +25658,8 @@ "releases": [ { "tag_name": "dev", - "published_at": "2024-10-18T19:06:13Z", - "tag_sha": "432a765356a28d883f2bbc54db83d60d82759d68", + "published_at": "2024-10-23T14:07:47Z", + "tag_sha": "e9be7e38b5242a8840f01830e272e8aaafa784eb", "has_schema": true, "doc_files": [ "docs/output.md", @@ -27825,13 +27833,13 @@ "deployments_url": "https://api.github.com/repos/bigbio/quantms/deployments", "created_at": "2021-10-27T18:13:00Z", "updated_at": "2024-10-09T13:50:47Z", - "pushed_at": "2024-10-20T19:27:53Z", + "pushed_at": "2024-10-23T16:25:00Z", "git_url": "git://github.com/bigbio/quantms.git", "ssh_url": "git@github.com:bigbio/quantms.git", "clone_url": "https://github.com/bigbio/quantms.git", "svn_url": "https://github.com/bigbio/quantms", "homepage": "https://quantms.org", - "size": 49641, + "size": 49644, "stargazers_count": 32, "watchers_count": 32, "language": "Nextflow", @@ -27845,7 +27853,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 55, + "open_issues_count": 54, "license": { "key": "mit", "name": "MIT License", @@ -27865,7 +27873,7 @@ ], "visibility": "public", "forks": 35, - "open_issues": 55, + "open_issues": 54, "watchers": 32, "default_branch": "master" }, @@ -27938,13 +27946,13 @@ "deployments_url": "https://api.github.com/repos/bigbio/quantms/deployments", "created_at": "2021-10-27T18:13:00Z", "updated_at": "2024-10-09T13:50:47Z", - "pushed_at": "2024-10-20T19:27:53Z", + "pushed_at": "2024-10-23T16:25:00Z", "git_url": "git://github.com/bigbio/quantms.git", "ssh_url": "git@github.com:bigbio/quantms.git", "clone_url": "https://github.com/bigbio/quantms.git", "svn_url": "https://github.com/bigbio/quantms", "homepage": "https://quantms.org", - "size": 49641, + "size": 49644, "stargazers_count": 32, "watchers_count": 32, "language": "Nextflow", @@ -27958,7 +27966,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 55, + "open_issues_count": 54, "license": { "key": "mit", "name": "MIT License", @@ -27978,7 +27986,7 @@ ], "visibility": "public", "forks": 35, - "open_issues": 55, + "open_issues": 54, "watchers": 32, "default_branch": "master" }, @@ -31615,12 +31623,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", - "updated_at": "2024-10-21T03:05:06Z", - "pushed_at": "2024-10-23T13:58:58Z", + "updated_at": "2024-10-23T19:23:18Z", + "pushed_at": "2024-10-23T21:55:22Z", "homepage": "https://nf-co.re/rnaseq", - "size": 72360, - "stargazers_count": 886, - "watchers_count": 886, + "size": 72359, + "stargazers_count": 888, + "watchers_count": 888, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -31631,7 +31639,7 @@ "forks_count": 702, "archived": false, "disabled": false, - "open_issues_count": 65, + "open_issues_count": 67, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -31641,8 +31649,8 @@ ], "visibility": "public", "forks": 702, - "open_issues": 65, - "watchers": 886, + "open_issues": 67, + "watchers": 888, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -31746,7 +31754,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 11, + "open_pr_count": 13, "repository_url": "https://github.com/nf-core/rnaseq", "contributors": [ { @@ -33745,8 +33753,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-23T13:58:55Z", - "tag_sha": "facaabdb9dea9d923cbe18d1a7ad90f1bc322d85", + "published_at": "2024-10-23T19:34:24Z", + "tag_sha": "1c5d2673ee47b966c8b80bcfe73ebe09ec53f0b2", "has_schema": true, "doc_files": [ "docs/output.md", @@ -34830,12 +34838,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/sarek", "created_at": "2019-04-30T15:43:00Z", - "updated_at": "2024-10-23T06:21:40Z", + "updated_at": "2024-10-23T17:38:18Z", "pushed_at": "2024-10-23T11:58:22Z", "homepage": "https://nf-co.re/sarek", "size": 92054, - "stargazers_count": 402, - "watchers_count": 402, + "stargazers_count": 403, + "watchers_count": 403, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -34866,7 +34874,7 @@ "visibility": "public", "forks": 404, "open_issues": 284, - "watchers": 402, + "watchers": 403, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -34901,7 +34909,7 @@ } }, "network_count": 404, - "subscribers_count": 129, + "subscribers_count": 128, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -37358,12 +37366,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/scdownstream", "created_at": "2024-06-11T06:38:31Z", - "updated_at": "2024-10-22T03:22:24Z", + "updated_at": "2024-10-23T17:06:58Z", "pushed_at": "2024-10-18T06:02:39Z", "homepage": "https://nf-co.re/scdownstream", "size": 1910, - "stargazers_count": 35, - "watchers_count": 35, + "stargazers_count": 36, + "watchers_count": 36, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -37374,7 +37382,7 @@ "forks_count": 9, "archived": false, "disabled": false, - "open_issues_count": 19, + "open_issues_count": 20, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -37388,8 +37396,8 @@ ], "visibility": "public", "forks": 9, - "open_issues": 19, - "watchers": 35, + "open_issues": 20, + "watchers": 36, "default_branch": "dev", "temp_clone_token": "", "allow_squash_merge": true, @@ -37973,7 +37981,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 5, + "forks_count": 6, "archived": false, "disabled": false, "open_issues_count": 2, @@ -37988,7 +37996,7 @@ "single-cell" ], "visibility": "public", - "forks": 5, + "forks": 6, "open_issues": 2, "watchers": 21, "default_branch": "master", @@ -38022,7 +38030,7 @@ "status": "disabled" } }, - "network_count": 5, + "network_count": 6, "subscribers_count": 18, "team_contributors_permission_push": true, "team_contributors_permission_admin": false,