diff --git a/.cache.tar.xz b/.cache.tar.xz index a4ccea7d76..f997cde2f2 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index ca4a3c1985..29cc41b4e3 100644 --- a/public/components.json +++ b/public/components.json @@ -3998,6 +3998,10 @@ "name": "rnafusion", "version": "3.0.1" }, + { + "name": "rnafusion", + "version": "3.0.1" + }, { "name": "rnafusion", "version": "3.0.1" @@ -37385,6 +37389,10 @@ "name": "rnadnavar", "version": "dev" }, + { + "name": "rnadnavar", + "version": "dev" + }, { "name": "rnadnavar", "version": "dev" @@ -38810,6 +38818,10 @@ "name": "rnadnavar", "version": "dev" }, + { + "name": "rnadnavar", + "version": "dev" + }, { "name": "rnadnavar", "version": "dev" @@ -43387,6 +43399,10 @@ "name": "rnadnavar", "version": "dev" }, + { + "name": "rnadnavar", + "version": "dev" + }, { "name": "rnadnavar", "version": "dev" @@ -97038,6 +97054,78 @@ ] } }, + { + "name": "seqkit_concat", + "path": "modules/nf-core/seqkit/concat/meta.yml", + "type": "module", + "meta": { + "name": "seqkit_concat", + "description": "Concatenating multiple uncompressed sequence files together", + "keywords": [ + "concat", + "fasta", + "fastq", + "merge" + ], + "tools": [ + { + "seqkit": { + "description": "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.\n", + "homepage": "https://github.com/shenwei356/seqkit", + "documentation": "https://bioinf.shenwei.me/seqkit/", + "tool_dev_url": "https://github.com/shenwei356/seqkit", + "doi": "10.1371/journal.pone.0163962", + "licence": [ + "MIT" + ] + } + } + ], + "input": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "input": { + "type": "file", + "description": "Sequence file in fasta/q format", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" + } + } + ], + "output": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n" + } + }, + { + "fastx": { + "type": "file", + "description": "A concatenated sequence file", + "pattern": "*.{fasta,fastq,fa,fq,fas,fna,faa}" + } + }, + { + "versions": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ], + "authors": [ + "@DLBPointon" + ], + "maintainers": [ + "@DLBPointon" + ] + } + }, { "name": "seqkit_fx2tab", "path": "modules/nf-core/seqkit/fx2tab/meta.yml", @@ -122362,6 +122450,10 @@ "name": "fetchngs", "version": "1.11.0" }, + { + "name": "fetchngs", + "version": "1.11.0" + }, { "name": "fetchngs", "version": "1.11.0" @@ -123203,6 +123295,10 @@ "name": "fetchngs", "version": "1.11.0" }, + { + "name": "fetchngs", + "version": "1.11.0" + }, { "name": "fetchngs", "version": "1.11.0" @@ -124077,6 +124173,10 @@ "name": "fetchngs", "version": "1.11.0" }, + { + "name": "fetchngs", + "version": "1.11.0" + }, { "name": "fetchngs", "version": "1.11.0" diff --git a/public/pipelines.json b/public/pipelines.json index 6114635ab0..4897b23fcd 100644 --- a/public/pipelines.json +++ b/public/pipelines.json @@ -11,9 +11,9 @@ "url": "https://api.github.com/repos/nf-core/airrflow", "created_at": "2018-12-04T11:39:05Z", "updated_at": "2024-01-25T05:20:30Z", - "pushed_at": "2024-02-08T14:54:25Z", + "pushed_at": "2024-02-09T12:09:32Z", "homepage": "https://nf-co.re/airrflow", - "size": 6472, + "size": 6479, "stargazers_count": 40, "watchers_count": 40, "language": "Nextflow", @@ -309,7 +309,7 @@ "url": "https://api.github.com/repos/nf-core/ampliseq", "created_at": "2018-09-26T15:24:54Z", "updated_at": "2024-02-08T15:41:50Z", - "pushed_at": "2024-02-08T12:57:16Z", + "pushed_at": "2024-02-09T09:22:54Z", "homepage": "https://nf-co.re/ampliseq", "size": 13707, "stargazers_count": 147, @@ -357,7 +357,7 @@ "contributors": [ { "name": "d4straub", - "count": 1020, + "count": 1321, "avatar_url": "https://avatars.githubusercontent.com/u/42973691?v=4" }, { @@ -3329,7 +3329,7 @@ "url": "https://api.github.com/repos/nf-core/crisprseq", "created_at": "2022-07-14T11:14:34Z", "updated_at": "2024-02-07T09:30:40Z", - "pushed_at": "2024-02-07T08:30:54Z", + "pushed_at": "2024-02-09T13:58:39Z", "homepage": "https://nf-co.re/crisprseq", "size": 5476, "stargazers_count": 19, @@ -6138,10 +6138,10 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/eager", "created_at": "2018-06-03T15:52:24Z", - "updated_at": "2024-01-29T11:17:56Z", - "pushed_at": "2024-02-08T14:07:45Z", + "updated_at": "2024-02-09T10:59:38Z", + "pushed_at": "2024-02-09T13:58:25Z", "homepage": "https://nf-co.re/eager", - "size": 66330, + "size": 66834, "stargazers_count": 117, "watchers_count": 117, "language": "Nextflow", @@ -6154,7 +6154,7 @@ "forks_count": 72, "archived": false, "disabled": false, - "open_issues_count": 62, + "open_issues_count": 57, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -6169,13 +6169,13 @@ ], "visibility": "public", "forks": 72, - "open_issues": 62, + "open_issues": 57, "watchers": 117, "default_branch": "master", "custom_properties": {}, "network_count": 72, "subscribers_count": 134, - "open_pr_count": 7, + "open_pr_count": 8, "contributors": [ { "name": "jfy133", @@ -7383,9 +7383,9 @@ "url": "https://api.github.com/repos/nf-core/funcscan", "created_at": "2021-12-13T10:35:54Z", "updated_at": "2024-01-25T05:18:28Z", - "pushed_at": "2024-02-08T14:47:39Z", + "pushed_at": "2024-02-09T11:33:03Z", "homepage": "https://nf-co.re/funcscan", - "size": 12600, + "size": 12619, "stargazers_count": 49, "watchers_count": 49, "language": "Nextflow", @@ -7398,7 +7398,7 @@ "forks_count": 14, "archived": false, "disabled": false, - "open_issues_count": 23, + "open_issues_count": 19, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -7421,13 +7421,13 @@ ], "visibility": "public", "forks": 14, - "open_issues": 23, + "open_issues": 19, "watchers": 49, "default_branch": "master", "custom_properties": {}, "network_count": 14, "subscribers_count": 67, - "open_pr_count": 3, + "open_pr_count": 2, "contributors": [ { "name": "jfy133", @@ -7816,8 +7816,8 @@ }, { "tag_name": "dev", - "published_at": "2024-01-31T16:41:32Z", - "tag_sha": "0ffba2202193afe848b6a4295920a93e40e531a2", + "published_at": "2024-02-09T11:33:02Z", + "tag_sha": "fb8489298240c03aa55db84b9c0c37685fecb45b", "has_schema": true, "doc_files": [ "docs/output.md", @@ -7986,16 +7986,16 @@ "count": 121, "avatar_url": "https://avatars.githubusercontent.com/u/15652539?v=4" }, + { + "name": "d4straub", + "count": 6, + "avatar_url": "https://avatars.githubusercontent.com/u/42973691?v=4" + }, { "name": "muffato", "count": 4, "avatar_url": "https://avatars.githubusercontent.com/u/623458?v=4" }, - { - "name": "d4straub", - "count": 2, - "avatar_url": "https://avatars.githubusercontent.com/u/42973691?v=4" - }, { "name": "drpatelh", "count": 1, @@ -10147,7 +10147,7 @@ "url": "https://api.github.com/repos/nf-core/mag", "created_at": "2018-05-22T06:06:58Z", "updated_at": "2024-02-08T08:55:53Z", - "pushed_at": "2024-02-09T00:00:47Z", + "pushed_at": "2024-02-09T13:35:15Z", "homepage": "https://nf-co.re/mag", "size": 19477, "stargazers_count": 170, @@ -10162,7 +10162,7 @@ "forks_count": 94, "archived": false, "disabled": false, - "open_issues_count": 48, + "open_issues_count": 44, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -10178,13 +10178,13 @@ ], "visibility": "public", "forks": 94, - "open_issues": 48, + "open_issues": 44, "watchers": 170, "default_branch": "master", "custom_properties": {}, "network_count": 94, "subscribers_count": 132, - "open_pr_count": 2, + "open_pr_count": 3, "contributors": [ { "name": "skrakau", @@ -11499,9 +11499,9 @@ "url": "https://api.github.com/repos/nf-core/metatdenovo", "created_at": "2021-10-19T18:58:24Z", "updated_at": "2024-02-08T05:52:29Z", - "pushed_at": "2024-02-08T15:03:57Z", + "pushed_at": "2024-02-09T12:07:30Z", "homepage": "https://nf-co.re/metatdenovo", - "size": 13714, + "size": 13731, "stargazers_count": 5, "watchers_count": 5, "language": "Nextflow", @@ -11536,7 +11536,7 @@ }, { "name": "erikrikarddaniel", - "count": 193, + "count": 199, "avatar_url": "https://avatars.githubusercontent.com/u/1520576?v=4" }, { @@ -11553,8 +11553,8 @@ "releases": [ { "tag_name": "dev", - "published_at": "2024-02-08T15:03:53Z", - "tag_sha": "88cf82c28a7119a640c8baf3cb79b7a06ca66603", + "published_at": "2024-02-09T12:07:27Z", + "tag_sha": "54cb246adaadd0dbf276de61ae6b0cfeb81bcfa1", "has_schema": true, "doc_files": [ "docs/output.md", @@ -13134,12 +13134,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/nanostring", "created_at": "2022-01-10T14:24:34Z", - "updated_at": "2024-01-25T02:16:40Z", + "updated_at": "2024-02-09T11:01:19Z", "pushed_at": "2024-02-07T13:09:28Z", "homepage": "https://nf-co.re/nanostring", "size": 2817, - "stargazers_count": 7, - "watchers_count": 7, + "stargazers_count": 9, + "watchers_count": 9, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -13147,7 +13147,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 2, + "forks_count": 4, "archived": false, "disabled": false, "open_issues_count": 6, @@ -13159,12 +13159,12 @@ "nanostringnorm" ], "visibility": "public", - "forks": 2, + "forks": 4, "open_issues": 6, - "watchers": 7, + "watchers": 9, "default_branch": "master", "custom_properties": {}, - "network_count": 2, + "network_count": 4, "subscribers_count": 133, "open_pr_count": 3, "contributors": [ @@ -13789,7 +13789,7 @@ "url": "https://api.github.com/repos/nf-core/pangenome", "created_at": "2020-11-08T18:02:43Z", "updated_at": "2024-02-07T15:39:23Z", - "pushed_at": "2024-02-08T12:22:00Z", + "pushed_at": "2024-02-09T11:46:02Z", "homepage": "https://nf-co.re/pangenome", "size": 3892, "stargazers_count": 41, @@ -16924,7 +16924,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 634, + "forks_count": 635, "archived": false, "disabled": false, "open_issues_count": 94, @@ -16936,14 +16936,14 @@ "rna-seq" ], "visibility": "public", - "forks": 634, + "forks": 635, "open_issues": 94, "watchers": 729, "default_branch": "master", "custom_properties": { "slack": "https://nfcore.slack.com/archives/CE8SSJV3N" }, - "network_count": 634, + "network_count": 635, "subscribers_count": 133, "open_pr_count": 11, "contributors": [ @@ -18914,12 +18914,12 @@ "fork": false, "url": "https://api.github.com/repos/nf-core/rnavar", "created_at": "2021-05-12T07:25:10Z", - "updated_at": "2024-02-07T09:28:55Z", + "updated_at": "2024-02-09T11:01:23Z", "pushed_at": "2024-02-08T16:01:02Z", "homepage": "https://nf-co.re/rnavar", "size": 3742, - "stargazers_count": 24, - "watchers_count": 24, + "stargazers_count": 26, + "watchers_count": 26, "language": "Nextflow", "has_issues": true, "has_projects": true, @@ -18927,7 +18927,7 @@ "has_wiki": false, "has_pages": false, "has_discussions": false, - "forks_count": 25, + "forks_count": 27, "archived": false, "disabled": false, "open_issues_count": 42, @@ -18942,12 +18942,12 @@ "worflow" ], "visibility": "public", - "forks": 25, + "forks": 27, "open_issues": 42, - "watchers": 24, + "watchers": 26, "default_branch": "master", "custom_properties": {}, - "network_count": 25, + "network_count": 27, "subscribers_count": 79, "open_pr_count": 3, "contributors": [ @@ -22444,9 +22444,9 @@ "url": "https://api.github.com/repos/nf-core/smrnaseq", "created_at": "2018-07-11T14:56:59Z", "updated_at": "2024-02-07T08:43:11Z", - "pushed_at": "2024-02-08T16:27:30Z", + "pushed_at": "2024-02-09T10:57:03Z", "homepage": "https://nf-co.re/smrnaseq", - "size": 8095, + "size": 8163, "stargazers_count": 64, "watchers_count": 64, "language": "Nextflow", @@ -22459,7 +22459,7 @@ "forks_count": 110, "archived": false, "disabled": false, - "open_issues_count": 25, + "open_issues_count": 23, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -22469,13 +22469,13 @@ ], "visibility": "public", "forks": 110, - "open_issues": 25, + "open_issues": 23, "watchers": 64, "default_branch": "master", "custom_properties": {}, "network_count": 110, "subscribers_count": 123, - "open_pr_count": 3, + "open_pr_count": 1, "contributors": [ { "name": "apeltzer", @@ -22821,8 +22821,8 @@ }, { "tag_name": "dev", - "published_at": "2024-02-05T09:54:56Z", - "tag_sha": "3ef02e76c75263916402c4dae12eb2788efef634", + "published_at": "2024-02-09T10:57:00Z", + "tag_sha": "18ae224be1d7d1067ee5a9fb10da633e5db2e2e1", "has_schema": true, "doc_files": [ "docs/output.md", @@ -24141,7 +24141,7 @@ "url": "https://api.github.com/repos/nf-core/viralrecon", "created_at": "2020-03-30T11:14:12Z", "updated_at": "2024-01-25T05:30:54Z", - "pushed_at": "2024-02-01T11:00:09Z", + "pushed_at": "2024-02-09T12:40:23Z", "homepage": "https://nf-co.re/viralrecon", "size": 10042, "stargazers_count": 105, @@ -24156,7 +24156,7 @@ "forks_count": 95, "archived": false, "disabled": false, - "open_issues_count": 35, + "open_issues_count": 36, "allow_forking": true, "is_template": false, "web_commit_signoff_required": false, @@ -24179,13 +24179,13 @@ ], "visibility": "public", "forks": 95, - "open_issues": 35, + "open_issues": 36, "watchers": 105, "default_branch": "master", "custom_properties": {}, "network_count": 95, "subscribers_count": 76, - "open_pr_count": 3, + "open_pr_count": 4, "contributors": [ { "name": "drpatelh",