diff --git a/.cache.tar.xz b/.cache.tar.xz index e29bafcb92..f03b68be81 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 10f952fe32..8b128092b5 100644 --- a/public/components.json +++ b/public/components.json @@ -7592,6 +7592,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -24675,6 +24679,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -106193,6 +106205,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" diff --git a/public/pipelines.json b/public/pipelines.json index b05870944b..aa777683b2 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -2038,7 +2038,7 @@ "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, @@ -2054,7 +2054,7 @@ ], "visibility": "public", "forks": 41, - "open_issues": 18, + "open_issues": 19, "watchers": 60, "default_branch": "master", "temp_clone_token": "", @@ -3630,12 +3630,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/chipseq", "created_at": "2018-04-24T15:42:59Z", - "updated_at": "2024-09-03T14:02:19Z", + "updated_at": "2024-10-01T02:56:18Z", "pushed_at": "2024-09-30T12:06:13Z", "homepage": "https://nf-co.re/chipseq", "size": 16478, - "stargazers_count": 186, - "watchers_count": 186, + "stargazers_count": 187, + "watchers_count": 187, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -3646,7 +3646,7 @@ "forks_count": 145, "archived": false, "disabled": false, - "open_issues_count": 11, + "open_issues_count": 12, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -3659,8 +3659,8 @@ ], "visibility": "public", "forks": 145, - "open_issues": 11, - "watchers": 186, + "open_issues": 12, + "watchers": 187, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -5232,14 +5232,14 @@ "forks_count": 8, "archived": false, "disabled": false, - "open_issues_count": 5, + "open_issues_count": 6, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 8, - "open_issues": 5, + "open_issues": 6, "watchers": 6, "default_branch": "dev", "temp_clone_token": "", @@ -8096,12 +8096,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/demultiplex", "created_at": "2020-03-05T15:48:10Z", - "updated_at": "2024-09-30T21:42:16Z", + "updated_at": "2024-10-01T06:28:16Z", "pushed_at": "2024-09-30T20:19:21Z", "homepage": "https://nf-co.re/demultiplex", "size": 13734, - "stargazers_count": 42, - "watchers_count": 42, + "stargazers_count": 43, + "watchers_count": 43, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -8112,7 +8112,7 @@ "forks_count": 36, "archived": false, "disabled": false, - "open_issues_count": 22, + "open_issues_count": 23, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -8125,8 +8125,8 @@ ], "visibility": "public", "forks": 36, - "open_issues": 22, - "watchers": 42, + "open_issues": 23, + "watchers": 43, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -8159,7 +8159,7 @@ } }, "network_count": 36, - "subscribers_count": 88, + "subscribers_count": 89, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9858,9 +9858,9 @@ "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": "2024-09-20T16:52:25Z", + "pushed_at": "2024-10-01T13:36:23Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 8512, + "size": 8521, "stargazers_count": 57, "watchers_count": 57, "language": "Nextflow", @@ -10636,7 +10636,7 @@ "forks_count": 80, "archived": false, "disabled": false, - "open_issues_count": 45, + "open_issues_count": 46, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10651,7 +10651,7 @@ ], "visibility": "public", "forks": 80, - "open_issues": 45, + "open_issues": 46, "watchers": 143, "default_branch": "master", "temp_clone_token": "", @@ -19812,14 +19812,14 @@ "forks_count": 5, "archived": false, "disabled": false, - "open_issues_count": 12, + "open_issues_count": 15, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 5, - "open_issues": 12, + "open_issues": 15, "watchers": 8, "default_branch": "dev", "temp_clone_token": "", @@ -20017,7 +20017,7 @@ "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/metapep", "contributors": [ { @@ -22157,10 +22157,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/multiplesequencealign", "created_at": "2023-07-24T14:30:12Z", - "updated_at": "2024-09-25T08:56:24Z", - "pushed_at": "2024-09-30T17:08:25Z", + "updated_at": "2024-10-01T08:25:42Z", + "pushed_at": "2024-10-01T08:25:37Z", "homepage": "https://nf-co.re/multiplesequencealign", - "size": 15142, + "size": 15144, "stargazers_count": 13, "watchers_count": 13, "language": "Nextflow", @@ -22173,14 +22173,14 @@ "forks_count": 11, "archived": false, "disabled": false, - "open_issues_count": 4, + "open_issues_count": 3, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 11, - "open_issues": 4, + "open_issues": 3, "watchers": 13, "default_branch": "dev", "temp_clone_token": "", @@ -22293,12 +22293,12 @@ "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/multiplesequencealign", "contributors": [ { "name": "luisas", - "count": 455, + "count": 473, "avatar_url": "https://avatars.githubusercontent.com/u/23131457?v=4" }, { @@ -22328,9 +22328,9 @@ } ], "released_after_tools": false, - "head_sha": "15c3126ec605dd661ef11773da7751516f9a076c", + "head_sha": "0df116a737e2fe8c75adcad66a276e65787f3b79", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/multiplesequencealign/compare/15c3126ec605dd661ef11773da7751516f9a076c...undefined", + "last_release_vs_default_compare_url": "https://github.com/nf-core/multiplesequencealign/compare/0df116a737e2fe8c75adcad66a276e65787f3b79...undefined", "commits_to_dev": 30, "is_DSL2": true, "has_nf_test": true, @@ -22339,13 +22339,13 @@ "nf-validation" ], "dev_nextflow_config_plugins": [ - "nf-validation@0.3.1" + "nf-validation@1.1.4" ], "releases": [ { "tag_name": "dev", - "published_at": "2024-09-25T08:56:20Z", - "tag_sha": "15c3126ec605dd661ef11773da7751516f9a076c", + "published_at": "2024-10-01T08:25:37Z", + "tag_sha": "0df116a737e2fe8c75adcad66a276e65787f3b79", "has_schema": true, "doc_files": [ "docs/output.md", @@ -23996,9 +23996,9 @@ "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": "2024-09-30T00:16:11Z", + "pushed_at": "2024-10-01T02:56:16Z", "homepage": "https://nf-co.re/oncoanalyser", - "size": 4917, + "size": 4932, "stargazers_count": 40, "watchers_count": 40, "language": "Nextflow", @@ -25742,14 +25742,14 @@ "forks_count": 12, "archived": false, "disabled": false, - "open_issues_count": 13, + "open_issues_count": 14, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 12, - "open_issues": 13, + "open_issues": 14, "watchers": 16, "default_branch": "dev", "temp_clone_token": "", @@ -25812,7 +25812,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": false, - "open_pr_count": 1, + "open_pr_count": 2, "repository_url": "https://github.com/nf-core/phaseimpute", "contributors": [ { @@ -26506,7 +26506,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 35, + "forks_count": 36, "archived": false, "disabled": false, "open_issues_count": 10, @@ -26521,7 +26521,7 @@ "protein-structure" ], "visibility": "public", - "forks": 35, + "forks": 36, "open_issues": 10, "watchers": 51, "default_branch": "master", @@ -26555,7 +26555,7 @@ "status": "disabled" } }, - "network_count": 35, + "network_count": 36, "subscribers_count": 156, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -27195,7 +27195,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 52, + "open_issues_count": 51, "license": { "key": "mit", "name": "MIT License", @@ -27215,7 +27215,7 @@ ], "visibility": "public", "forks": 35, - "open_issues": 52, + "open_issues": 51, "watchers": 30, "default_branch": "master" }, @@ -27307,7 +27307,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 52, + "open_issues_count": 51, "license": { "key": "mit", "name": "MIT License", @@ -27327,7 +27327,7 @@ ], "visibility": "public", "forks": 35, - "open_issues": 52, + "open_issues": 51, "watchers": 30, "default_branch": "master" }, @@ -27950,9 +27950,9 @@ "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": "2024-09-30T12:41:20Z", + "pushed_at": "2024-10-01T12:08:52Z", "homepage": "https://nf-co.re/raredisease", - "size": 13468, + "size": 13514, "stargazers_count": 84, "watchers_count": 84, "language": "Nextflow", @@ -28993,8 +28993,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-26T08:09:46Z", - "tag_sha": "7da78ba97cb3edc69d583d55fd6a5d2fb35e8fb4", + "published_at": "2024-10-01T12:08:35Z", + "tag_sha": "166269a05129f5f1b3531f683af17146d5236786", "has_schema": true, "doc_files": [ "docs/output.md", @@ -29023,7 +29023,7 @@ "chromograph", "cnvnator_cnvnator", "cnvnator_convert2vcf", - "deepvariant", + "deepvariant_rundeepvariant", "eklipse", "ensemblvep_filtervep", "ensemblvep_vep", @@ -30959,7 +30959,7 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", - "updated_at": "2024-09-30T01:09:22Z", + "updated_at": "2024-10-01T12:47:46Z", "pushed_at": "2024-09-30T15:47:07Z", "homepage": "https://nf-co.re/rnaseq", "size": 71550, @@ -33479,12 +33479,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/rnavar", "created_at": "2021-05-12T07:25:10Z", - "updated_at": "2024-09-18T22:24:28Z", + "updated_at": "2024-10-01T02:55:47Z", "pushed_at": "2024-08-28T10:35:25Z", "homepage": "https://nf-co.re/rnavar", "size": 3930, - "stargazers_count": 34, - "watchers_count": 34, + "stargazers_count": 35, + "watchers_count": 35, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -33492,7 +33492,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 31, + "forks_count": 32, "archived": false, "disabled": false, "open_issues_count": 41, @@ -33507,9 +33507,9 @@ "worflow" ], "visibility": "public", - "forks": 31, + "forks": 32, "open_issues": 41, - "watchers": 34, + "watchers": 35, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -33541,7 +33541,7 @@ "status": "disabled" } }, - "network_count": 31, + "network_count": 32, "subscribers_count": 104, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -34000,9 +34000,9 @@ "url": "https://api.github.com/repos/nf-core/sarek", "created_at": "2019-04-30T15:43:00Z", "updated_at": "2024-09-24T20:50:42Z", - "pushed_at": "2024-09-30T08:16:37Z", + "pushed_at": "2024-10-01T09:16:49Z", "homepage": "https://nf-co.re/sarek", - "size": 91904, + "size": 91959, "stargazers_count": 393, "watchers_count": 393, "language": "Nextflow", @@ -34015,7 +34015,7 @@ "forks_count": 403, "archived": false, "disabled": false, - "open_issues_count": 277, + "open_issues_count": 276, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -34034,7 +34034,7 @@ ], "visibility": "public", "forks": 403, - "open_issues": 277, + "open_issues": 276, "watchers": 393, "default_branch": "master", "temp_clone_token": "", @@ -36396,8 +36396,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-30T08:16:37Z", - "tag_sha": "4c664f454a0cc97e875380f9dd6f94d44927b560", + "published_at": "2024-10-01T09:16:49Z", + "tag_sha": "6e7655f587d66c18fa727a863d68bb257ddb0ded", "has_schema": true, "doc_files": [ "docs/output.md", @@ -37342,12 +37342,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/scrnaseq", "created_at": "2019-04-08T13:12:00Z", - "updated_at": "2024-09-24T17:07:00Z", + "updated_at": "2024-10-01T06:38:16Z", "pushed_at": "2024-09-30T13:04:25Z", "homepage": "https://nf-co.re/scrnaseq", "size": 44034, - "stargazers_count": 209, - "watchers_count": 209, + "stargazers_count": 210, + "watchers_count": 210, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -37376,7 +37376,7 @@ "visibility": "public", "forks": 166, "open_issues": 47, - "watchers": 209, + "watchers": 210, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -39237,7 +39237,7 @@ "forks_count": 124, "archived": false, "disabled": false, - "open_issues_count": 19, + "open_issues_count": 20, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -39247,7 +39247,7 @@ ], "visibility": "public", "forks": 124, - "open_issues": 19, + "open_issues": 20, "watchers": 72, "default_branch": "master", "temp_clone_token": "", @@ -39335,7 +39335,7 @@ "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/smrnaseq", "contributors": [ { @@ -40460,12 +40460,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/taxprofiler", "created_at": "2022-02-18T06:56:10Z", - "updated_at": "2024-09-30T14:50:04Z", - "pushed_at": "2024-09-27T09:02:05Z", + "updated_at": "2024-10-01T02:53:37Z", + "pushed_at": "2024-10-01T09:31:57Z", "homepage": "https://nf-co.re/taxprofiler", - "size": 14721, - "stargazers_count": 125, - "watchers_count": 125, + "size": 14722, + "stargazers_count": 126, + "watchers_count": 126, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -40476,7 +40476,7 @@ "forks_count": 35, "archived": false, "disabled": false, - "open_issues_count": 44, + "open_issues_count": 43, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -40495,8 +40495,8 @@ ], "visibility": "public", "forks": 35, - "open_issues": 44, - "watchers": 125, + "open_issues": 43, + "watchers": 126, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -40783,7 +40783,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 5, + "open_pr_count": 4, "repository_url": "https://github.com/nf-core/taxprofiler", "contributors": [ { @@ -41599,8 +41599,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-26T09:28:18Z", - "tag_sha": "7d7d0c7d4c55926daa2851c09d70c4e25e9ec912", + "published_at": "2024-10-01T09:31:55Z", + "tag_sha": "7e4734a31f821f6125a89e34f7a9f2c2e76cd2bd", "has_schema": true, "doc_files": [ "docs/output.md",