diff --git a/.cache.tar.xz b/.cache.tar.xz index d543efd818..e29bafcb92 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 29cbcf717f..10f952fe32 100644 --- a/public/components.json +++ b/public/components.json @@ -7588,6 +7588,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -24663,6 +24667,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -106177,6 +106189,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -144976,14 +144992,14 @@ { "truth_bed": { "type": "file", - "description": "A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)", + "description": "A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) This input should be used to provide the golden truth BED files.", "pattern": "*.bed" } }, { - "evaluation_bed": { + "regions_bed": { "type": "file", - "description": "A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)", + "description": "A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) This input should be used to provide the regions used by the analysis", "pattern": "*.bed" } } diff --git a/public/pipelines.json b/public/pipelines.json index f847eb2b12..b05870944b 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -8096,12 +8096,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/demultiplex", "created_at": "2020-03-05T15:48:10Z", - "updated_at": "2024-09-03T19:19:28Z", - "pushed_at": "2024-09-24T14:47:30Z", + "updated_at": "2024-09-30T21:42:16Z", + "pushed_at": "2024-09-30T20:19:21Z", "homepage": "https://nf-co.re/demultiplex", - "size": 13648, - "stargazers_count": 41, - "watchers_count": 41, + "size": 13734, + "stargazers_count": 42, + "watchers_count": 42, "language": "Nextflow", "has_issues": true, "has_projects": false, @@ -8112,7 +8112,7 @@ "forks_count": 36, "archived": false, "disabled": false, - "open_issues_count": 24, + "open_issues_count": 22, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -8125,8 +8125,8 @@ ], "visibility": "public", "forks": 36, - "open_issues": 24, - "watchers": 41, + "open_issues": 22, + "watchers": 42, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -8206,7 +8206,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 3, + "open_pr_count": 1, "repository_url": "https://github.com/nf-core/demultiplex", "contributors": [ { @@ -8627,8 +8627,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-23T14:56:38Z", - "tag_sha": "1a26f26803054a73f7caf8cb6694dd354f84ef02", + "published_at": "2024-09-30T20:19:21Z", + "tag_sha": "73df4a57a4c6b156d1da4fd5274064ad84719bb1", "has_schema": true, "doc_files": [ "docs/output.md", @@ -9539,12 +9539,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/diaproteomics", "created_at": "2019-11-08T13:16:02Z", - "updated_at": "2024-09-03T10:14:45Z", + "updated_at": "2024-09-30T18:22:04Z", "pushed_at": "2024-05-09T11:41:56Z", "homepage": "https://nf-co.re/diaproteomics", "size": 4261, - "stargazers_count": 13, - "watchers_count": 13, + "stargazers_count": 14, + "watchers_count": 14, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -9568,7 +9568,7 @@ "visibility": "public", "forks": 12, "open_issues": 7, - "watchers": 13, + "watchers": 14, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -12068,12 +12068,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/fetchngs", "created_at": "2021-06-03T09:26:41Z", - "updated_at": "2024-09-26T19:10:06Z", + "updated_at": "2024-09-30T18:44:14Z", "pushed_at": "2024-09-24T20:27:23Z", "homepage": "https://nf-co.re/fetchngs", "size": 4026, - "stargazers_count": 148, - "watchers_count": 148, + "stargazers_count": 149, + "watchers_count": 149, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -12100,7 +12100,7 @@ "visibility": "public", "forks": 72, "open_issues": 29, - "watchers": 148, + "watchers": 149, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false, @@ -18714,7 +18714,7 @@ } }, "network_count": 4, - "subscribers_count": 177, + "subscribers_count": 176, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -22158,9 +22158,9 @@ "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": "2024-09-25T13:28:26Z", + "pushed_at": "2024-09-30T17:08:25Z", "homepage": "https://nf-co.re/multiplesequencealign", - "size": 13810, + "size": 15142, "stargazers_count": 13, "watchers_count": 13, "language": "Nextflow", @@ -23095,9 +23095,9 @@ "url": "https://api.github.com/repos/nf-core/nascent", "created_at": "2018-11-15T15:46:09Z", "updated_at": "2024-09-06T05:39:17Z", - "pushed_at": "2024-09-30T12:38:28Z", + "pushed_at": "2024-09-30T17:11:17Z", "homepage": "https://nf-co.re/nascent", - "size": 8574, + "size": 8579, "stargazers_count": 18, "watchers_count": 18, "language": "Nextflow", @@ -24281,7 +24281,7 @@ } }, "network_count": 2, - "subscribers_count": 187, + "subscribers_count": 185, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -27174,7 +27174,7 @@ "releases_url": "https://api.github.com/repos/bigbio/quantms/releases{/id}", "deployments_url": "https://api.github.com/repos/bigbio/quantms/deployments", "created_at": "2021-10-27T18:13:00Z", - "updated_at": "2024-09-12T17:07:39Z", + "updated_at": "2024-09-30T22:02:16Z", "pushed_at": "2024-09-19T19:21:02Z", "git_url": "git://github.com/bigbio/quantms.git", "ssh_url": "git@github.com:bigbio/quantms.git", @@ -27182,8 +27182,8 @@ "svn_url": "https://github.com/bigbio/quantms", "homepage": "https://quantms.org", "size": 49322, - "stargazers_count": 29, - "watchers_count": 29, + "stargazers_count": 30, + "watchers_count": 30, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -27195,7 +27195,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 51, + "open_issues_count": 52, "license": { "key": "mit", "name": "MIT License", @@ -27215,8 +27215,8 @@ ], "visibility": "public", "forks": 35, - "open_issues": 51, - "watchers": 29, + "open_issues": 52, + "watchers": 30, "default_branch": "master" }, "source": { @@ -27286,7 +27286,7 @@ "releases_url": "https://api.github.com/repos/bigbio/quantms/releases{/id}", "deployments_url": "https://api.github.com/repos/bigbio/quantms/deployments", "created_at": "2021-10-27T18:13:00Z", - "updated_at": "2024-09-12T17:07:39Z", + "updated_at": "2024-09-30T22:02:16Z", "pushed_at": "2024-09-19T19:21:02Z", "git_url": "git://github.com/bigbio/quantms.git", "ssh_url": "git@github.com:bigbio/quantms.git", @@ -27294,8 +27294,8 @@ "svn_url": "https://github.com/bigbio/quantms", "homepage": "https://quantms.org", "size": 49322, - "stargazers_count": 29, - "watchers_count": 29, + "stargazers_count": 30, + "watchers_count": 30, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -27307,7 +27307,7 @@ "mirror_url": null, "archived": false, "disabled": false, - "open_issues_count": 51, + "open_issues_count": 52, "license": { "key": "mit", "name": "MIT License", @@ -27327,8 +27327,8 @@ ], "visibility": "public", "forks": 35, - "open_issues": 51, - "watchers": 29, + "open_issues": 52, + "watchers": 30, "default_branch": "master" }, "security_and_analysis": { @@ -30960,9 +30960,9 @@ "url": "https://api.github.com/repos/nf-core/rnaseq", "created_at": "2018-03-29T13:10:58Z", "updated_at": "2024-09-30T01:09:22Z", - "pushed_at": "2024-09-20T15:52:33Z", + "pushed_at": "2024-09-30T15:47:07Z", "homepage": "https://nf-co.re/rnaseq", - "size": 71422, + "size": 71550, "stargazers_count": 874, "watchers_count": 874, "language": "Nextflow", @@ -30975,7 +30975,7 @@ "forks_count": 697, "archived": false, "disabled": false, - "open_issues_count": 66, + "open_issues_count": 67, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -30985,7 +30985,7 @@ ], "visibility": "public", "forks": 697, - "open_issues": 66, + "open_issues": 67, "watchers": 874, "default_branch": "master", "temp_clone_token": "", @@ -31090,7 +31090,7 @@ "TEMPLATE_branch_protection_enforce_admins": -1, "TEMPLATE_restrict_push": true, "has_required_topics": true, - "open_pr_count": 11, + "open_pr_count": 12, "repository_url": "https://github.com/nf-core/rnaseq", "contributors": [ { @@ -32909,8 +32909,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-20T15:52:33Z", - "tag_sha": "e6e85efa364e54bea859db3060033043dadb9dea", + "published_at": "2024-09-30T15:47:06Z", + "tag_sha": "fcbfa1b8bf9c1ef1877b9deaba2317e9e5737ad5", "has_schema": true, "doc_files": [ "docs/output.md", @@ -33020,7 +33020,7 @@ "forks_count": 24, "archived": false, "disabled": false, - "open_issues_count": 11, + "open_issues_count": 12, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -33032,7 +33032,7 @@ ], "visibility": "public", "forks": 24, - "open_issues": 11, + "open_issues": 12, "watchers": 42, "default_branch": "master", "temp_clone_token": "", @@ -38225,7 +38225,7 @@ } }, "network_count": 14, - "subscribers_count": 172, + "subscribers_count": 171, "team_contributors_permission_push": true, "team_contributors_permission_admin": false, "team_core_permission_push": true, @@ -39222,9 +39222,9 @@ "url": "https://api.github.com/repos/nf-core/smrnaseq", "created_at": "2018-07-11T14:56:59Z", "updated_at": "2024-09-12T18:37:55Z", - "pushed_at": "2024-09-27T15:19:18Z", + "pushed_at": "2024-09-30T15:06:28Z", "homepage": "https://nf-co.re/smrnaseq", - "size": 8722, + "size": 8763, "stargazers_count": 72, "watchers_count": 72, "language": "Nextflow", @@ -39237,7 +39237,7 @@ "forks_count": 124, "archived": false, "disabled": false, - "open_issues_count": 18, + "open_issues_count": 19, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -39247,7 +39247,7 @@ ], "visibility": "public", "forks": 124, - "open_issues": 18, + "open_issues": 19, "watchers": 72, "default_branch": "master", "temp_clone_token": "", @@ -39786,8 +39786,8 @@ }, { "tag_name": "dev", - "published_at": "2024-09-27T15:19:18Z", - "tag_sha": "adc43dbbe5ce454939aeb7e3717b24d75b44e5c8", + "published_at": "2024-09-30T15:06:28Z", + "tag_sha": "f1768c53b642041a3fef5f947231c0549bd794fa", "has_schema": true, "doc_files": [ "docs/output.md", @@ -39801,7 +39801,6 @@ "bowtie_build", "bowtie2_align", "bowtie2_build", - "cat_cat", "cat_fastq", "csvtk_join", "fastp", @@ -39815,7 +39814,6 @@ "mirtop_stats", "mirtrace_qc", "multiqc", - "pigz_uncompress", "samtools_flagstat", "samtools_idxstats", "samtools_index", @@ -40462,12 +40460,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/taxprofiler", "created_at": "2022-02-18T06:56:10Z", - "updated_at": "2024-09-30T00:31:49Z", + "updated_at": "2024-09-30T14:50:04Z", "pushed_at": "2024-09-27T09:02:05Z", "homepage": "https://nf-co.re/taxprofiler", "size": 14721, - "stargazers_count": 124, - "watchers_count": 124, + "stargazers_count": 125, + "watchers_count": 125, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -40498,7 +40496,7 @@ "visibility": "public", "forks": 35, "open_issues": 44, - "watchers": 124, + "watchers": 125, "default_branch": "master", "temp_clone_token": "", "allow_squash_merge": false,