diff --git a/.cache.tar.xz b/.cache.tar.xz index 81e529b9be..47837f966a 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 59ab366dc6..9691463dcd 100644 --- a/public/components.json +++ b/public/components.json @@ -7672,6 +7672,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -25103,6 +25107,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -106836,6 +106848,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" diff --git a/public/pipelines.json b/public/pipelines.json index 6d0b030945..c0f814faed 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -73,7 +73,7 @@ } }, "network_count": 34, - "subscribers_count": 142, + "subscribers_count": 143, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -591,7 +591,7 @@ } }, "network_count": 115, - "subscribers_count": 143, + "subscribers_count": 144, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -1500,7 +1500,7 @@ } }, "network_count": 116, - "subscribers_count": 142, + "subscribers_count": 143, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -2088,7 +2088,7 @@ } }, "network_count": 41, - "subscribers_count": 142, + "subscribers_count": 143, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -2544,7 +2544,7 @@ } }, "network_count": 30, - "subscribers_count": 135, + "subscribers_count": 136, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -2796,7 +2796,7 @@ } }, "network_count": 13, - "subscribers_count": 149, + "subscribers_count": 150, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -3151,7 +3151,7 @@ } }, "network_count": 12, - "subscribers_count": 138, + "subscribers_count": 139, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -3422,7 +3422,7 @@ } }, "network_count": 3, - "subscribers_count": 146, + "subscribers_count": 147, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -3646,7 +3646,7 @@ "forks_count": 145, "archived": false, "disabled": false, - "open_issues_count": 13, + "open_issues_count": 14, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -3659,7 +3659,7 @@ ], "visibility": "public", "forks": 145, - "open_issues": 13, + "open_issues": 14, "watchers": 189, "default_branch": "master", "temp_clone_token": "", @@ -3693,7 +3693,7 @@ } }, "network_count": 145, - "subscribers_count": 140, + "subscribers_count": 141, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -3757,7 +3757,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 4, "repository_url": "https://github.com/nf-core/chipseq", "contributors": [ { @@ -4105,9 +4105,9 @@ "url": "https://api.github.com/repos/nf-core/circdna", "created_at": "2021-11-02T09:45:33Z", "updated_at": "2024-09-03T10:14:57Z", - "pushed_at": "2024-10-08T12:29:58Z", + "pushed_at": "2024-10-10T08:16:51Z", "homepage": "https://nf-co.re/circdna", - "size": 192968, + "size": 192977, "stargazers_count": 28, "watchers_count": 28, "language": "Python", @@ -4171,7 +4171,7 @@ } }, "network_count": 14, - "subscribers_count": 148, + "subscribers_count": 149, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -4555,7 +4555,7 @@ "url": "https://api.github.com/repos/nf-core/circrna", "created_at": "2021-02-10T14:28:49Z", "updated_at": "2024-09-26T13:31:31Z", - "pushed_at": "2024-10-09T16:45:42Z", + "pushed_at": "2024-10-10T10:33:26Z", "homepage": "https://nf-co.re/circrna", "size": 73598, "stargazers_count": 44, @@ -4621,7 +4621,7 @@ } }, "network_count": 21, - "subscribers_count": 103, + "subscribers_count": 104, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -4899,7 +4899,7 @@ } }, "network_count": 27, - "subscribers_count": 107, + "subscribers_count": 108, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -5122,7 +5122,7 @@ } }, "network_count": 2, - "subscribers_count": 69, + "subscribers_count": 70, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -5360,7 +5360,7 @@ } }, "network_count": 7, - "subscribers_count": 151, + "subscribers_count": 152, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -5507,9 +5507,9 @@ "url": "https://api.github.com/repos/nf-core/createtaxdb", "created_at": "2023-10-24T08:41:35Z", "updated_at": "2024-10-09T09:11:02Z", - "pushed_at": "2024-10-10T06:50:00Z", + "pushed_at": "2024-10-10T11:27:02Z", "homepage": "https://nf-co.re/createtaxdb", - "size": 3130, + "size": 3147, "stargazers_count": 7, "watchers_count": 7, "language": "Nextflow", @@ -5519,10 +5519,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 3, + "forks_count": 4, "archived": false, "disabled": false, - "open_issues_count": 17, + "open_issues_count": 18, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -5535,8 +5535,8 @@ "taxonomic-profiling" ], "visibility": "public", - "forks": 3, - "open_issues": 17, + "forks": 4, + "open_issues": 18, "watchers": 7, "default_branch": "dev", "temp_clone_token": "", @@ -5569,8 +5569,8 @@ "status": "disabled" } }, - "network_count": 3, - "subscribers_count": 161, + "network_count": 4, + "subscribers_count": 162, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -5639,7 +5639,7 @@ "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/createtaxdb", "contributors": [ { @@ -5781,7 +5781,7 @@ } }, "network_count": 25, - "subscribers_count": 137, + "subscribers_count": 138, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -6211,7 +6211,7 @@ } }, "network_count": 5, - "subscribers_count": 137, + "subscribers_count": 138, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -6409,7 +6409,7 @@ } }, "network_count": 46, - "subscribers_count": 149, + "subscribers_count": 150, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -7014,7 +7014,7 @@ } }, "network_count": 3, - "subscribers_count": 190, + "subscribers_count": 191, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -7998,9 +7998,9 @@ "url": "https://api.github.com/repos/nf-core/demo", "created_at": "2024-05-05T12:11:15Z", "updated_at": "2024-09-26T12:16:09Z", - "pushed_at": "2024-10-09T11:05:34Z", + "pushed_at": "2024-10-10T10:54:47Z", "homepage": "https://nf-co.re/demo", - "size": 514, + "size": 555, "stargazers_count": 3, "watchers_count": 3, "language": "Nextflow", @@ -8058,7 +8058,7 @@ } }, "network_count": 6, - "subscribers_count": 185, + "subscribers_count": 186, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -8246,7 +8246,7 @@ } }, "network_count": 36, - "subscribers_count": 88, + "subscribers_count": 89, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9261,7 +9261,7 @@ } }, "network_count": 2, - "subscribers_count": 183, + "subscribers_count": 184, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9435,7 +9435,7 @@ "url": "https://api.github.com/repos/nf-core/detaxizer", "created_at": "2023-10-30T14:11:55Z", "updated_at": "2024-09-03T11:25:15Z", - "pushed_at": "2024-10-09T11:05:41Z", + "pushed_at": "2024-10-10T10:38:46Z", "homepage": "https://nf-co.re/detaxizer", "size": 5538, "stargazers_count": 13, @@ -9447,10 +9447,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 4, + "forks_count": 5, "archived": false, "disabled": false, - "open_issues_count": 2, + "open_issues_count": 4, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -9471,8 +9471,8 @@ "taxonomic-profiling" ], "visibility": "public", - "forks": 4, - "open_issues": 2, + "forks": 5, + "open_issues": 4, "watchers": 13, "default_branch": "master", "temp_clone_token": "", @@ -9505,8 +9505,8 @@ "status": "disabled" } }, - "network_count": 4, - "subscribers_count": 162, + "network_count": 5, + "subscribers_count": 163, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9560,7 +9560,7 @@ "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/detaxizer", "contributors": [ { @@ -9724,7 +9724,7 @@ } }, "network_count": 12, - "subscribers_count": 67, + "subscribers_count": 68, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9981,9 +9981,9 @@ "url": "https://api.github.com/repos/nf-core/differentialabundance", "created_at": "2022-10-12T08:49:25Z", "updated_at": "2024-09-25T10:45:18Z", - "pushed_at": "2024-10-09T22:31:42Z", + "pushed_at": "2024-10-10T09:38:52Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 8487, + "size": 8526, "stargazers_count": 57, "watchers_count": 57, "language": "Nextflow", @@ -9996,7 +9996,7 @@ "forks_count": 33, "archived": false, "disabled": false, - "open_issues_count": 45, + "open_issues_count": 44, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10014,7 +10014,7 @@ ], "visibility": "public", "forks": 33, - "open_issues": 45, + "open_issues": 44, "watchers": 57, "default_branch": "master", "temp_clone_token": "", @@ -10048,7 +10048,7 @@ } }, "network_count": 33, - "subscribers_count": 141, + "subscribers_count": 142, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -10112,7 +10112,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 6, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/differentialabundance", "contributors": [ { @@ -10587,7 +10587,7 @@ } }, "network_count": 0, - "subscribers_count": 219, + "subscribers_count": 220, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -12882,12 +12882,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/funcscan", "created_at": "2021-12-13T10:35:54Z", - "updated_at": "2024-10-08T04:25:53Z", + "updated_at": "2024-10-10T10:48:04Z", "pushed_at": "2024-10-09T11:05:18Z", "homepage": "https://nf-co.re/funcscan", "size": 18653, - "stargazers_count": 71, - "watchers_count": 71, + "stargazers_count": 72, + "watchers_count": 72, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -12922,7 +12922,7 @@ "visibility": "public", "forks": 20, "open_issues": 14, - "watchers": 71, + "watchers": 72, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -17594,10 +17594,10 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 107, + "forks_count": 108, "archived": false, "disabled": false, - "open_issues_count": 63, + "open_issues_count": 66, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -17612,8 +17612,8 @@ "nanopore-sequencing" ], "visibility": "public", - "forks": 107, - "open_issues": 63, + "forks": 108, + "open_issues": 66, "watchers": 209, "default_branch": "master", "temp_clone_token": "", @@ -17646,7 +17646,7 @@ "status": "disabled" } }, - "network_count": 107, + "network_count": 108, "subscribers_count": 153, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -17791,7 +17791,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 7, + "open_pr_count": 8, "repository_url": "https://github.com/nf-core/mag", "contributors": [ { @@ -20916,7 +20916,7 @@ "forks_count": 143, "archived": false, "disabled": false, - "open_issues_count": 46, + "open_issues_count": 47, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -20932,7 +20932,7 @@ ], "visibility": "public", "forks": 143, - "open_issues": 46, + "open_issues": 47, "watchers": 137, "default_branch": "master", "temp_clone_token": "", @@ -22524,9 +22524,9 @@ "url": "https://api.github.com/repos/nf-core/multiplesequencealign", "created_at": "2023-07-24T14:30:12Z", "updated_at": "2024-10-07T12:15:15Z", - "pushed_at": "2024-10-09T11:06:36Z", + "pushed_at": "2024-10-10T07:50:39Z", "homepage": "https://nf-co.re/multiplesequencealign", - "size": 15193, + "size": 15199, "stargazers_count": 17, "watchers_count": 17, "language": "Nextflow", @@ -22539,14 +22539,14 @@ "forks_count": 11, "archived": false, "disabled": false, - "open_issues_count": 3, + "open_issues_count": 5, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 11, - "open_issues": 3, + "open_issues": 5, "watchers": 17, "default_branch": "master", "temp_clone_token": "", @@ -22754,8 +22754,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-01T08:25:37Z", - "tag_sha": "0df116a737e2fe8c75adcad66a276e65787f3b79", + "published_at": "2024-10-10T07:50:39Z", + "tag_sha": "2510a0b2356c4f0d71e3aa9cc447bb68868f4207", "has_schema": true, "doc_files": [ "docs/output.md", @@ -24406,9 +24406,9 @@ "url": "https://api.github.com/repos/nf-core/oncoanalyser", "created_at": "2022-12-22T05:01:49Z", "updated_at": "2024-09-15T18:34:09Z", - "pushed_at": "2024-10-10T06:54:10Z", + "pushed_at": "2024-10-10T07:17:15Z", "homepage": "https://nf-co.re/oncoanalyser", - "size": 5105, + "size": 5112, "stargazers_count": 40, "watchers_count": 40, "language": "Nextflow", @@ -24627,9 +24627,9 @@ "url": "https://api.github.com/repos/nf-core/pairgenomealign", "created_at": "2024-05-24T01:40:57Z", "updated_at": "2024-10-09T07:32:26Z", - "pushed_at": "2024-10-10T01:06:28Z", + "pushed_at": "2024-10-10T07:19:28Z", "homepage": "https://nf-co.re/pairgenomealign", - "size": 1797, + "size": 1813, "stargazers_count": 6, "watchers_count": 6, "language": "Nextflow", @@ -24642,7 +24642,7 @@ "forks_count": 2, "archived": false, "disabled": false, - "open_issues_count": 3, + "open_issues_count": 1, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -24657,7 +24657,7 @@ ], "visibility": "public", "forks": 2, - "open_issues": 3, + "open_issues": 1, "watchers": 6, "default_branch": "master", "temp_clone_token": "", @@ -24755,7 +24755,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": false, - "open_pr_count": 2, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/pairgenomealign", "contributors": [ { @@ -24781,7 +24781,7 @@ "nf-validation@1.1.3" ], "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" + "nf-schema@2.1.1" ], "releases": [ { @@ -24844,8 +24844,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-09T00:17:22Z", - "tag_sha": "6974029eced4844b1f93a5244fd7b0879b91157c", + "published_at": "2024-10-10T07:19:28Z", + "tag_sha": "1cfa9c5b350b669f7b1114b8e610b6feb3923c48", "has_schema": true, "doc_files": [ "docs/output.md", @@ -24867,7 +24867,7 @@ "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", - "utils_nfvalidation_plugin" + "utils_nfschema_plugin" ] } } @@ -26933,9 +26933,9 @@ "url": "https://api.github.com/repos/nf-core/proteinfold", "created_at": "2022-03-03T10:41:35Z", "updated_at": "2024-09-18T22:25:36Z", - "pushed_at": "2024-10-09T11:08:17Z", + "pushed_at": "2024-10-10T09:44:26Z", "homepage": "https://nf-co.re/proteinfold", - "size": 6348, + "size": 6406, "stargazers_count": 51, "watchers_count": 51, "language": "Nextflow", @@ -27140,7 +27140,7 @@ "nf-validation@1.1.3" ], "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" + "nf-schema@2.1.1" ], "releases": [ { @@ -27216,8 +27216,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-08T21:21:30Z", - "tag_sha": "b3ecf98e1120169d76a741c9bc0cbb67b7b7bae2", + "published_at": "2024-10-10T09:44:26Z", + "tag_sha": "5270d2e782a55b4c0413dbd6e464b8cae1e403e9", "has_schema": true, "doc_files": [ "docs/output.md", @@ -27236,7 +27236,7 @@ "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", - "utils_nfvalidation_plugin" + "utils_nfschema_plugin" ] } } @@ -28390,9 +28390,9 @@ "url": "https://api.github.com/repos/nf-core/raredisease", "created_at": "2021-06-21T09:40:29Z", "updated_at": "2024-09-18T12:29:08Z", - "pushed_at": "2024-10-09T11:08:46Z", + "pushed_at": "2024-10-10T09:41:26Z", "homepage": "https://nf-co.re/raredisease", - "size": 13522, + "size": 13535, "stargazers_count": 84, "watchers_count": 84, "language": "Nextflow", @@ -28405,7 +28405,7 @@ "forks_count": 34, "archived": false, "disabled": false, - "open_issues_count": 34, + "open_issues_count": 35, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -28421,7 +28421,7 @@ ], "visibility": "public", "forks": 34, - "open_issues": 34, + "open_issues": 35, "watchers": 84, "default_branch": "master", "temp_clone_token": "", @@ -28501,11 +28501,11 @@ "strict": true, "contexts": [ "nf-core", - "Run pipeline with test data (latest-everything, -profile test,docker)", - "Run pipeline with test data (latest-everything, -profile test_one_sample,docker)", - "Run pipeline with test data (23.04.0, -profile test,docker)", - "Run pipeline with test data (23.04.0, -profile test_one_sample,docker)", - "pre-commit" + "pre-commit", + "Run pipeline with test data (24.04.2, -profile test)", + "Run pipeline with test data (24.04.2, -profile test_one_sample)", + "Run pipeline with test data (latest-everything, -profile test)", + "Run pipeline with test data (latest-everything, -profile test_one_sample)" ], "contexts_url": "https://api.github.com/repos/nf-core/raredisease/branches/dev/protection/required_status_checks/contexts", "checks": [ @@ -28514,23 +28514,23 @@ "app_id": 15368 }, { - "context": "Run pipeline with test data (latest-everything, -profile test,docker)", + "context": "pre-commit", "app_id": 15368 }, { - "context": "Run pipeline with test data (latest-everything, -profile test_one_sample,docker)", + "context": "Run pipeline with test data (24.04.2, -profile test)", "app_id": 15368 }, { - "context": "Run pipeline with test data (23.04.0, -profile test,docker)", + "context": "Run pipeline with test data (24.04.2, -profile test_one_sample)", "app_id": 15368 }, { - "context": "Run pipeline with test data (23.04.0, -profile test_one_sample,docker)", + "context": "Run pipeline with test data (latest-everything, -profile test)", "app_id": 15368 }, { - "context": "pre-commit", + "context": "Run pipeline with test data (latest-everything, -profile test_one_sample)", "app_id": 15368 } ] @@ -28549,7 +28549,7 @@ "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/raredisease", "contributors": [ { @@ -29820,14 +29820,14 @@ "forks_count": 4, "archived": false, "disabled": false, - 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