diff --git a/.cache.tar.xz b/.cache.tar.xz index 5a4dff89b2..715ab95406 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index ee745b53c1..cfcc36c3a8 100644 --- a/public/components.json +++ b/public/components.json @@ -8041,6 +8041,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -26179,6 +26183,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -109429,6 +109441,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" diff --git a/public/pipelines.json b/public/pipelines.json index aafbc0b3a2..7540151e15 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -5688,9 +5688,9 @@ "url": "https://api.github.com/repos/nf-core/crisprseq", "created_at": "2022-07-14T11:14:34Z", "updated_at": "2024-11-04T06:20:10Z", - "pushed_at": "2024-10-29T11:39:41Z", + "pushed_at": "2024-11-08T13:46:33Z", "homepage": "https://nf-co.re/crisprseq", - "size": 19229, + "size": 19248, "stargazers_count": 29, "watchers_count": 29, "language": "Nextflow", @@ -5703,7 +5703,7 @@ "forks_count": 26, "archived": false, "disabled": false, - "open_issues_count": 25, + "open_issues_count": 24, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -5715,7 +5715,7 @@ ], "visibility": "public", "forks": 26, - "open_issues": 25, + "open_issues": 24, "watchers": 29, "default_branch": "master", "temp_clone_token": "", @@ -5789,7 +5789,7 @@ "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/crisprseq", "contributors": [ { @@ -6072,8 +6072,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-29T11:39:41Z", - "tag_sha": "eacc5e7ea3591d05352b7799d8c0090fb5b35392", + "published_at": "2024-11-08T13:46:33Z", + "tag_sha": "72afaab9739305b1b56ab3651a7811df3ec5e6f7", "has_schema": true, "doc_files": [ "docs/output.md", @@ -6319,12 +6319,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/cutandrun", "created_at": "2021-01-14T11:47:23Z", - "updated_at": "2024-10-16T00:23:42Z", + "updated_at": "2024-11-08T08:42:05Z", "pushed_at": "2024-10-11T12:33:02Z", "homepage": "https://nf-co.re/cutandrun", "size": 9067, - "stargazers_count": 81, - "watchers_count": 81, + "stargazers_count": 80, + "watchers_count": 80, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -6348,7 +6348,7 @@ "visibility": "public", "forks": 47, "open_issues": 28, - "watchers": 81, + "watchers": 80, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -6986,7 +6986,7 @@ } }, "network_count": 3, - "subscribers_count": 194, + "subscribers_count": 193, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -9473,7 +9473,7 @@ "forks_count": 3, "archived": false, "disabled": false, - "open_issues_count": 4, + "open_issues_count": 5, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -9484,7 +9484,7 @@ ], "visibility": "public", "forks": 3, - "open_issues": 4, + "open_issues": 5, "watchers": 3, "default_branch": "master", "temp_clone_token": "", @@ -9763,7 +9763,7 @@ } }, "network_count": 5, - "subscribers_count": 168, + "subscribers_count": 167, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -10238,9 +10238,9 @@ "url": "https://api.github.com/repos/nf-core/differentialabundance", "created_at": "2022-10-12T08:49:25Z", "updated_at": "2024-11-07T08:59:29Z", - "pushed_at": "2024-11-07T13:05:49Z", + "pushed_at": "2024-11-08T09:31:47Z", "homepage": "https://nf-co.re/differentialabundance", - "size": 9097, + "size": 8932, "stargazers_count": 63, "watchers_count": 63, "language": "Nextflow", @@ -10253,7 +10253,7 @@ "forks_count": 36, "archived": false, "disabled": false, - "open_issues_count": 59, + "open_issues_count": 60, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10271,7 +10271,7 @@ ], "visibility": "public", "forks": 36, - "open_issues": 59, + "open_issues": 60, "watchers": 63, "default_branch": "master", "temp_clone_token": "", @@ -10725,8 +10725,8 @@ }, { "tag_name": "dev", - "published_at": "2024-11-07T13:05:49Z", - "tag_sha": "1fa3df52f6e5336536e493708a6b5995fbac4bbe", + "published_at": "2024-11-08T09:31:47Z", + "tag_sha": "1fc81012b42d7630c99d9e6ebc952e1547b17c96", "has_schema": true, "doc_files": [ "docs/output.md", @@ -10844,7 +10844,7 @@ } }, "network_count": 0, - "subscribers_count": 216, + "subscribers_count": 215, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -11170,9 +11170,9 @@ "url": "https://api.github.com/repos/nf-core/eager", "created_at": "2018-06-03T15:52:24Z", "updated_at": "2024-11-03T18:20:21Z", - "pushed_at": "2024-10-25T14:14:43Z", + "pushed_at": "2024-11-08T11:26:28Z", "homepage": "https://nf-co.re/eager", - "size": 67494, + "size": 67503, "stargazers_count": 148, "watchers_count": 148, "language": "Nextflow", @@ -14646,7 +14646,7 @@ "forks_count": 8, "archived": false, "disabled": false, - "open_issues_count": 37, + "open_issues_count": 36, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -14658,7 +14658,7 @@ ], "visibility": "public", "forks": 8, - "open_issues": 37, + "open_issues": 36, "watchers": 2, "default_branch": "dev", "temp_clone_token": "", @@ -14722,7 +14722,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": -1, "has_required_topics": false, - "open_pr_count": 6, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/genomeqc", "contributors": [ { @@ -21692,9 +21692,9 @@ "url": "https://api.github.com/repos/nf-core/methylseq", "created_at": "2018-03-12T15:46:42Z", "updated_at": "2024-10-27T07:44:12Z", - "pushed_at": "2024-11-06T18:31:10Z", + "pushed_at": "2024-11-08T10:01:31Z", "homepage": "https://nf-co.re/methylseq", - "size": 22498, + "size": 22497, "stargazers_count": 140, "watchers_count": 140, "language": "Nextflow", @@ -21704,7 +21704,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 144, + "forks_count": 145, "archived": false, "disabled": false, "open_issues_count": 33, @@ -21722,7 +21722,7 @@ "rrbs" ], "visibility": "public", - "forks": 144, + "forks": 145, "open_issues": 33, "watchers": 140, "default_branch": "master", @@ -21756,7 +21756,7 @@ "status": "disabled" } }, - "network_count": 144, + "network_count": 145, "subscribers_count": 149, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -23711,9 +23711,9 @@ "url": "https://api.github.com/repos/nf-core/nanoseq", "created_at": "2019-09-09T11:23:29Z", "updated_at": "2024-10-26T06:48:27Z", - "pushed_at": "2024-10-11T12:34:01Z", + "pushed_at": "2024-11-08T06:55:32Z", "homepage": "https://nf-co.re/nanoseq", - "size": 7106, + "size": 7112, "stargazers_count": 179, "watchers_count": 179, "language": "Nextflow", @@ -26222,7 +26222,7 @@ } }, "network_count": 5, - "subscribers_count": 171, + "subscribers_count": 170, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -27092,7 +27092,7 @@ "forks_count": 14, "archived": false, "disabled": false, - "open_issues_count": 17, + "open_issues_count": 18, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -27105,7 +27105,7 @@ ], "visibility": "public", "forks": 14, - "open_issues": 17, + "open_issues": 18, "watchers": 16, "default_branch": "dev", "temp_clone_token": "", @@ -27203,7 +27203,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": false, - "open_pr_count": 4, + "open_pr_count": 5, "repository_url": "https://github.com/nf-core/phaseimpute", "contributors": [ { @@ -29353,9 +29353,9 @@ "url": "https://api.github.com/repos/nf-core/raredisease", "created_at": "2021-06-21T09:40:29Z", "updated_at": "2024-11-05T12:20:30Z", - "pushed_at": "2024-11-06T15:25:46Z", + "pushed_at": "2024-11-08T10:45:51Z", "homepage": "https://nf-co.re/raredisease", - "size": 13686, + "size": 13697, "stargazers_count": 87, "watchers_count": 87, "language": "Nextflow", @@ -29368,7 +29368,7 @@ "forks_count": 34, "archived": false, "disabled": false, - "open_issues_count": 31, + "open_issues_count": 32, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -29384,7 +29384,7 @@ ], "visibility": "public", "forks": 34, - "open_issues": 31, + "open_issues": 32, "watchers": 87, "default_branch": "master", "temp_clone_token": "", @@ -29512,7 +29512,7 @@ "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/raredisease", "contributors": [ { @@ -30768,9 +30768,9 @@ "url": "https://api.github.com/repos/nf-core/reportho", "created_at": "2024-02-26T10:23:32Z", "updated_at": "2024-10-21T17:45:17Z", - "pushed_at": "2024-10-14T13:54:09Z", + "pushed_at": "2024-11-08T13:05:48Z", "homepage": "", - "size": 2195, + "size": 2248, "stargazers_count": 9, "watchers_count": 9, "language": "Nextflow", @@ -30783,14 +30783,14 @@ "forks_count": 4, "archived": false, "disabled": false, - "open_issues_count": 6, + "open_issues_count": 5, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, "topics": [], "visibility": "public", "forks": 4, - "open_issues": 6, + "open_issues": 5, "watchers": 9, "default_branch": "master", "temp_clone_token": "", @@ -30864,7 +30864,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": false, - "open_pr_count": 1, + "open_pr_count": 0, "repository_url": "https://github.com/nf-core/reportho", "contributors": [ { @@ -30950,8 +30950,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-14T13:54:09Z", - "tag_sha": "43b75294df4b08c60e34c46423815919d149ea4b", + "published_at": "2024-11-08T13:05:48Z", + "tag_sha": "05bf32b71375d263a4c0526cb4a11fab2c7da39e", "has_schema": true, "doc_files": [ "docs/output.md", @@ -30959,6 +30959,7 @@ ], "components": { "modules": [ + "cat_cat", "csvtk_concat", "csvtk_join", "fastme", @@ -32368,7 +32369,7 @@ "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", "updated_at": "2024-11-07T09:26:03Z", - "pushed_at": "2024-10-24T11:32:08Z", + "pushed_at": "2024-11-08T13:41:55Z", "homepage": "https://nf-co.re/rnaseq", "size": 72419, "stargazers_count": 904, @@ -32383,7 +32384,7 @@ "forks_count": 705, "archived": false, "disabled": false, - "open_issues_count": 71, + "open_issues_count": 70, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -32393,7 +32394,7 @@ ], "visibility": "public", "forks": 705, - "open_issues": 71, + "open_issues": 70, "watchers": 904, "default_branch": "master", "temp_clone_token": "", @@ -32498,7 +32499,7 @@ "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": [ { @@ -34587,12 +34588,17 @@ }, { "tag_name": "dev", - "published_at": "2024-10-24T09:58:21Z", - "tag_sha": "8cddc95676cc2d646f9cee08ec0241970b341175", + "published_at": "2024-11-08T13:41:55Z", + "tag_sha": "da5f13567f06460afedf220b4eef9597e9befd04", "has_schema": true, "doc_files": [ "docs/output.md", - "docs/usage.md" + "docs/usage.md", + "docs/usage/DEanalysis/de_rstudio.md", + "docs/usage/DEanalysis/index.md", + "docs/usage/DEanalysis/interpretation.md", + "docs/usage/DEanalysis/rnaseq.md", + "docs/usage/DEanalysis/theory.md" ], "components": { "modules": [ @@ -39111,12 +39117,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/scrnaseq", "created_at": "2019-04-08T13:12:00Z", - "updated_at": "2024-11-05T03:15:50Z", + "updated_at": "2024-11-08T12:51:14Z", "pushed_at": "2024-11-06T08:55:45Z", "homepage": "https://nf-co.re/scrnaseq", "size": 44182, - "stargazers_count": 212, - "watchers_count": 212, + "stargazers_count": 213, + "watchers_count": 213, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -39145,7 +39151,7 @@ "visibility": "public", "forks": 169, "open_issues": 56, - "watchers": 212, + "watchers": 213, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -41616,7 +41622,7 @@ "url": "https://api.github.com/repos/nf-core/spatialvi", "created_at": "2022-02-23T20:44:38Z", "updated_at": "2024-10-28T12:40:51Z", - "pushed_at": "2024-10-26T11:05:33Z", + "pushed_at": "2024-11-08T13:16:54Z", "homepage": "https://nf-co.re/spatialvi", "size": 7257, "stargazers_count": 51, @@ -41831,12 +41837,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/spatialxe", "created_at": "2024-03-14T10:57:36Z", - "updated_at": "2024-11-07T15:24:16Z", + "updated_at": "2024-11-08T06:32:19Z", "pushed_at": "2024-11-07T15:54:29Z", "homepage": "https://nf-co.re/spatialxe", "size": 2280, - "stargazers_count": 3, - "watchers_count": 3, + "stargazers_count": 4, + "watchers_count": 4, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -41855,7 +41861,7 @@ "visibility": "public", "forks": 2, "open_issues": 27, - "watchers": 3, + "watchers": 4, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": true, @@ -41888,7 +41894,7 @@ } }, "network_count": 2, - "subscribers_count": 229, + "subscribers_count": 218, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -43701,7 +43707,7 @@ } }, "network_count": 1, - "subscribers_count": 177, + "subscribers_count": 176, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -45087,9 +45093,9 @@ "url": "https://api.github.com/repos/nf-core/viralrecon", "created_at": "2020-03-30T11:14:12Z", "updated_at": "2024-10-21T17:46:31Z", - "pushed_at": "2024-10-25T16:23:20Z", + "pushed_at": "2024-11-08T12:12:35Z", "homepage": "https://nf-co.re/viralrecon", - "size": 10366, + "size": 10406, "stargazers_count": 122, "watchers_count": 122, "language": "Nextflow", @@ -45102,7 +45108,7 @@ "forks_count": 110, "archived": false, "disabled": false, - "open_issues_count": 35, + "open_issues_count": 34, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -45125,7 +45131,7 @@ ], "visibility": "public", "forks": 110, - "open_issues": 35, + "open_issues": 34, "watchers": 122, "default_branch": "master", "temp_clone_token": "", @@ -45223,7 +45229,7 @@ "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/viralrecon", "contributors": [ { @@ -45827,8 +45833,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-25T16:23:20Z", - "tag_sha": "402fad897779b39157a3de56469a7c3a5bfe98d0", + "published_at": "2024-11-08T12:12:35Z", + "tag_sha": "27b2c6cecdef50ada42f6547b5c1abb56fdf6f2a", "has_schema": true, "doc_files": [ "docs/output.md",