diff --git a/.cache.tar.xz b/.cache.tar.xz index 5c1e813b86..e4b6f4423f 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index da3ff4cd46..d08a550000 100644 --- a/public/components.json +++ b/public/components.json @@ -8405,6 +8405,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -27321,6 +27325,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -43925,9 +43937,7 @@ "description": "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin", "pattern": "*.tsv" } - } - ], - [ + }, { "proteins": { "type": "file", @@ -44057,10 +44067,10 @@ } }, { - "*.candidates.faa": { + "*_proteins.faa": { "type": "file", "description": "Output from prodigal if not already supplied", - "pattern": "*.proteins.faa" + "pattern": "*_proteins.faa" } } ] @@ -44074,10 +44084,10 @@ } }, { - "*.faa": { + "*.candidates.faa": { "type": "file", "description": "FAA file", - "pattern": "*.faa" + "pattern": "*.candidates.faa" } } ] @@ -106901,6 +106911,22 @@ "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" @@ -113075,6 +113101,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -131931,6 +131961,10 @@ "name": "viralrecon", "version": "2.6.0" }, + { + "name": "viralrecon", + "version": "2.6.0" + }, { "name": "viralrecon", "version": "2.6.0" @@ -133071,13 +133105,14 @@ { "meta": { "type": "map", - "description": "Groovy Map containing output information\n" + "description": "Groovy Map containing output information\n", + "pattern": "*.g.vcf" } }, { - "*.g.vcf*": { - "type": "file", - "description": "Indexed gvcf file", + "*.{idx,tbi}": { + "type": "map", + "description": "Groovy Map containing output information\n", "pattern": "*.g.vcf" } } @@ -205382,6 +205417,10 @@ "name": "phageannotator", "version": "dev" }, + { + "name": "phageannotator", + "version": "dev" + }, { "name": "phageannotator", "version": "dev" @@ -208936,6 +208975,10 @@ "name": "riboseq", "version": "1.0.1" }, + { + "name": "riboseq", + "version": "1.0.1" + }, { "name": "riboseq", "version": "1.0.1" @@ -209862,6 +209905,10 @@ "name": "crisprseq", "version": "2.3.0" }, + { + "name": "datasync", + "version": "dev" + }, { "name": "deepmodeloptim", "version": "dev" @@ -210053,10 +210100,6 @@ "name": "chipseq", "version": "2.1.0" }, - { - "name": "datasync", - "version": "dev" - }, { "name": "differentialabundance", "version": "1.5.0" diff --git a/public/pipelines.json b/public/pipelines.json index 59258ab3cb..3c92fb8f03 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -10,12 +10,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/airrflow", "created_at": "2018-12-04T11:39:05Z", - "updated_at": "2024-12-11T00:19:53Z", + "updated_at": "2024-12-11T05:42:29Z", "pushed_at": "2024-12-11T00:21:58Z", "homepage": "https://nf-co.re/airrflow", "size": 12586, - "stargazers_count": 54, - "watchers_count": 54, + "stargazers_count": 55, + "watchers_count": 55, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -40,7 +40,7 @@ "visibility": "public", "forks": 35, "open_issues": 23, - "watchers": 54, + "watchers": 55, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -580,7 +580,7 @@ "forks_count": 120, "archived": false, "disabled": false, - "open_issues_count": 34, + "open_issues_count": 33, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -603,7 +603,7 @@ ], "visibility": "public", "forks": 120, - "open_issues": 34, + "open_issues": 33, "watchers": 188, "default_branch": "master", "temp_clone_token": "", @@ -766,7 +766,7 @@ "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/ampliseq", "contributors": [ { @@ -6123,7 +6123,7 @@ "forks_count": 26, "archived": false, "disabled": false, - "open_issues_count": 24, + "open_issues_count": 23, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -6135,7 +6135,7 @@ ], "visibility": "public", "forks": 26, - "open_issues": 24, + "open_issues": 23, "watchers": 34, "default_branch": "master", "temp_clone_token": "", @@ -6209,7 +6209,7 @@ "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/crisprseq", "contributors": [ { @@ -7466,10 +7466,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/datasync", "created_at": "2024-02-26T10:30:52Z", - "updated_at": "2024-11-05T06:28:32Z", - "pushed_at": "2024-10-11T12:33:26Z", + "updated_at": "2024-12-11T10:47:59Z", + "pushed_at": "2024-12-11T13:38:44Z", "homepage": "https://nf-co.re/datasync", - "size": 506, + "size": 509, "stargazers_count": 8, "watchers_count": 8, "language": "Nextflow", @@ -7523,7 +7523,7 @@ } }, "network_count": 3, - "subscribers_count": 194, + "subscribers_count": 191, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -7594,13 +7594,18 @@ "name": "apeltzer", "count": 5, "avatar_url": "https://avatars.githubusercontent.com/u/2359510?v=4" + }, + { + "name": "grst", + "count": 2, + "avatar_url": "https://avatars.githubusercontent.com/u/7051479?v=4" } ], "released_after_tools": false, - "head_sha": "b0120a4b466ecca14ac4668eb14f6e47b08e31d0", + "head_sha": "daa8765856886120b6fb98612a8afe3d2d48d239", "last_release_is_head": false, - "last_release_vs_default_compare_url": "https://github.com/nf-core/datasync/compare/b0120a4b466ecca14ac4668eb14f6e47b08e31d0...undefined", - "commits_to_dev": 5, + "last_release_vs_default_compare_url": "https://github.com/nf-core/datasync/compare/daa8765856886120b6fb98612a8afe3d2d48d239...undefined", + "commits_to_dev": 14, "is_DSL2": true, "has_nf_test": false, "has_nf_test_dev": false, @@ -7618,7 +7623,7 @@ "doi": "" }, "dev_nextflow_config_plugins": [ - "nf-validation@1.1.3" + "nf-schema@2.1.1" ], "dev_nextflow_config_manifest": { "name": "nf-core/datasync", @@ -7626,15 +7631,15 @@ "homePage": "https://github.com/nf-core/datasync", "description": "", "mainScript": "main.nf", - "nextflowVersion": "!>=23.04.0", + "nextflowVersion": "!>=24.04.2", "version": "1.0dev", "doi": "" }, "releases": [ { "tag_name": "dev", - "published_at": "2024-02-26T10:51:44Z", - "tag_sha": "b0120a4b466ecca14ac4668eb14f6e47b08e31d0", + "published_at": "2024-12-11T10:47:53Z", + "tag_sha": "daa8765856886120b6fb98612a8afe3d2d48d239", "has_schema": true, "doc_files": [ "docs/output.md", @@ -7647,7 +7652,7 @@ "subworkflows": [ "utils_nextflow_pipeline", "utils_nfcore_pipeline", - "utils_nfvalidation_plugin" + "utils_nfschema_plugin" ] } } @@ -11094,7 +11099,7 @@ "forks_count": 37, "archived": false, "disabled": false, - "open_issues_count": 69, + "open_issues_count": 80, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -11112,7 +11117,7 @@ ], "visibility": "public", "forks": 37, - "open_issues": 69, + "open_issues": 80, "watchers": 66, "default_branch": "master", "temp_clone_token": "", @@ -11210,7 +11215,7 @@ "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": [ { @@ -11705,7 +11710,7 @@ } }, "network_count": 1, - "subscribers_count": 191, + "subscribers_count": 190, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -12083,9 +12088,9 @@ "url": "https://api.github.com/repos/nf-core/eager", "created_at": "2018-06-03T15:52:24Z", "updated_at": "2024-12-10T13:50:06Z", - "pushed_at": "2024-12-06T15:33:04Z", + "pushed_at": "2024-12-11T12:24:21Z", "homepage": "https://nf-co.re/eager", - "size": 66703, + "size": 66705, "stargazers_count": 151, "watchers_count": 151, "language": "Nextflow", @@ -14365,7 +14370,7 @@ "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": "2024-12-10T14:43:59Z", + "pushed_at": "2024-12-11T14:02:34Z", "homepage": "https://nf-co.re/funcscan", "size": 18610, "stargazers_count": 74, @@ -21359,7 +21364,7 @@ "url": "https://api.github.com/repos/nf-core/marsseq", "created_at": "2021-07-20T20:57:04Z", "updated_at": "2024-11-25T11:25:04Z", - "pushed_at": "2024-12-02T13:26:05Z", + "pushed_at": "2024-12-11T13:17:07Z", "homepage": "https://nf-co.re/marsseq", "size": 3462, "stargazers_count": 6, @@ -21671,8 +21676,8 @@ }, { "tag_name": "dev", - "published_at": "2024-12-02T13:25:55Z", - "tag_sha": "22c0b8745fac33374a5700bc13240da2fe70f72b", + "published_at": "2024-12-11T13:17:04Z", + "tag_sha": "dee2bdc462f929f8584fd58f3e1616f914a5b713", "has_schema": true, "doc_files": [ "docs/output.md", @@ -22657,9 +22662,9 @@ "url": "https://api.github.com/repos/nf-core/metatdenovo", "created_at": "2021-10-19T18:58:24Z", "updated_at": "2024-12-05T19:06:01Z", - "pushed_at": "2024-10-11T12:35:04Z", + "pushed_at": "2024-12-11T09:07:29Z", "homepage": "https://nf-co.re/metatdenovo", - "size": 13926, + "size": 13929, "stargazers_count": 23, "watchers_count": 23, "language": "Nextflow", @@ -22929,8 +22934,8 @@ }, { "tag_name": "dev", - "published_at": "2024-06-24T12:45:14Z", - "tag_sha": "78689bdfe9fe1226d2057bf32450e239ed2aeb8d", + "published_at": "2024-12-11T09:07:29Z", + "tag_sha": "c749cffb471a34f92d2b13fade09d2be6ff53827", "has_schema": true, "doc_files": [ "docs/output.md", @@ -25284,7 +25289,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 81, + "forks_count": 82, "archived": false, "disabled": false, "open_issues_count": 40, @@ -25298,7 +25303,7 @@ "qc" ], "visibility": "public", - "forks": 81, + "forks": 82, "open_issues": 40, "watchers": 184, "default_branch": "master", @@ -25332,7 +25337,7 @@ "status": "disabled" } }, - "network_count": 81, + "network_count": 82, "subscribers_count": 140, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -25708,7 +25713,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 8, + "forks_count": 9, "archived": false, "disabled": false, "open_issues_count": 5, @@ -25720,7 +25725,7 @@ "nanostringnorm" ], "visibility": "public", - "forks": 8, + "forks": 9, "open_issues": 5, "watchers": 13, "default_branch": "master", @@ -25754,7 +25759,7 @@ "status": "disabled" } }, - "network_count": 8, + "network_count": 9, "subscribers_count": 160, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -29628,9 +29633,9 @@ "url": "https://api.github.com/repos/nf-core/pixelator", "created_at": "2022-09-17T18:27:29Z", "updated_at": "2024-09-03T10:12:04Z", - "pushed_at": "2024-12-10T16:11:28Z", + "pushed_at": "2024-12-11T10:46:48Z", "homepage": "https://nf-co.re/pixelator", - "size": 4777, + "size": 4794, "stargazers_count": 8, "watchers_count": 8, "language": "Nextflow", @@ -29956,8 +29961,8 @@ }, { "tag_name": "dev", - "published_at": "2024-10-29T12:51:32Z", - "tag_sha": "a2a6c1c99fede0ad2634ba43b6da3e75787daf8e", + "published_at": "2024-12-11T10:36:19Z", + "tag_sha": "e1fd2143c117d418dfd193e535e9e3d5c118125c", "has_schema": true, "doc_files": [ "docs/output.md", @@ -33930,9 +33935,9 @@ "url": "https://api.github.com/repos/nf-core/rnafusion", "created_at": "2018-10-05T13:05:57Z", "updated_at": "2024-12-10T09:23:18Z", - "pushed_at": "2024-12-10T15:19:09Z", + "pushed_at": "2024-12-11T12:23:14Z", "homepage": "https://nf-co.re/rnafusion", - "size": 19826, + "size": 19853, "stargazers_count": 146, "watchers_count": 146, "language": "Nextflow", @@ -33945,7 +33950,7 @@ "forks_count": 98, "archived": false, "disabled": false, - "open_issues_count": 48, + "open_issues_count": 47, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -33958,7 +33963,7 @@ ], "visibility": "public", "forks": 98, - "open_issues": 48, + "open_issues": 47, "watchers": 146, "default_branch": "master", "temp_clone_token": "", @@ -34709,7 +34714,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 710, + "forks_count": 711, "archived": false, "disabled": false, "open_issues_count": 80, @@ -34721,7 +34726,7 @@ "rna-seq" ], "visibility": "public", - "forks": 710, + "forks": 711, "open_issues": 80, "watchers": 936, "default_branch": "master", @@ -34757,7 +34762,7 @@ "status": "disabled" } }, - "network_count": 710, + "network_count": 711, "subscribers_count": 158, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, @@ -38087,9 +38092,9 @@ "url": "https://api.github.com/repos/nf-core/sarek", "created_at": "2019-04-30T15:43:00Z", "updated_at": "2024-12-10T14:15:09Z", - "pushed_at": "2024-12-10T14:07:12Z", + "pushed_at": "2024-12-11T09:05:23Z", "homepage": "https://nf-co.re/sarek", - "size": 97896, + "size": 98821, "stargazers_count": 411, "watchers_count": 411, "language": "Nextflow", @@ -40498,8 +40503,8 @@ }, { "tag_name": "dev", - "published_at": "2024-12-10T13:35:33Z", - "tag_sha": "5c6be78611ff40a0390952ea4bab27cd3c9d52fa", + "published_at": "2024-12-11T09:05:21Z", + "tag_sha": "cd59770684043373c64539b9ae247ee77ca18566", "has_schema": true, "doc_files": [ "docs/output.md",