[automated] Update json files and markdown cache

nf-core · Sep 4, 2024 · 1892ba4 · 1892ba4
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Showing 3 changed files with 134 additions and 13 deletions.
diff --git a/.cache.tar.xz b/.cache.tar.xz
diff --git a/public/components.json b/public/components.json
@@ -5980,6 +5980,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -11726,6 +11730,107 @@
         }
       ]
     },
+    {
+      "name": "bcftools_plugintag2tag",
+      "path": "modules/nf-core/bcftools/plugintag2tag/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "bcftools_plugintag2tag",
+        "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.",
+        "keywords": [
+          "tag2tag",
+          "bcftools",
+          "VCF"
+        ],
+        "tools": [
+          {
+            "view": {
+              "description": "Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.\n",
+              "homepage": "http://samtools.github.io/bcftools/bcftools.html",
+              "documentation": "https://samtools.github.io/bcftools/howtos/plugin.tag2tag.html",
+              "doi": "10.1093/bioinformatics/btp352",
+              "licence": [
+                "MIT"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "The vcf file to be inspected.\ne.g. 'file.vcf'\n"
+            }
+          },
+          {
+            "index": {
+              "type": "file",
+              "description": "The tab index for the VCF file to be inspected.\ne.g. 'file.tbi'\n"
+            }
+          },
+          {
+            "regions": {
+              "type": "file",
+              "description": "Optionally, restrict the operation to regions listed in this file.\ne.g. 'file.vcf'\n"
+            }
+          },
+          {
+            "targets": {
+              "type": "file",
+              "description": "Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)\ne.g. 'file.vcf'\n"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "VCF normalized output file",
+              "pattern": "*.{vcf,vcf.gz,bcf,bcf.gz}"
+            }
+          },
+          {
+            "csi": {
+              "type": "file",
+              "description": "Default VCF file index",
+              "pattern": "*.csi"
+            }
+          },
+          {
+            "tbi": {
+              "type": "file",
+              "description": "Alternative VCF file index",
+              "pattern": "*.tbi"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@eweizy"
+        ],
+        "maintainers": [
+          "@eweizy"
+        ]
+      }
+    },
     {
       "name": "bcftools_query",
       "path": "modules/nf-core/bcftools/query/meta.yml",
@@ -19032,6 +19137,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -70489,6 +70602,10 @@
           "name": "isoseq",
           "version": "1.1.5"
         },
+        {
+          "name": "isoseq",
+          "version": "1.1.5"
+        },
         {
           "name": "isoseq",
           "version": "1.1.5"
@@ -81980,6 +82097,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"

diff --git a/public/pipelines.json b/public/pipelines.json
@@ -5639,7 +5639,7 @@
             "updated_at": "2024-09-03T12:35:24Z",
             "pushed_at": "2024-09-04T13:30:41Z",
             "homepage": "https://nf-co.re/crisprseq",
-            "size": 7402,
+            "size": 18722,
             "stargazers_count": 25,
             "watchers_count": 25,
             "language": "Nextflow",
@@ -19985,7 +19985,7 @@
             "updated_at": "2024-09-03T10:35:54Z",
             "pushed_at": "2024-09-04T13:35:26Z",
             "homepage": "https://nf-co.re/metatdenovo",
-            "size": 13887,
+            "size": 13891,
             "stargazers_count": 19,
             "watchers_count": 19,
             "language": "Nextflow",
@@ -22067,14 +22067,14 @@
             "forks_count": 10,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 3,
+            "open_issues_count": 4,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 10,
-            "open_issues": 3,
+            "open_issues": 4,
             "watchers": 13,
             "default_branch": "dev",
             "temp_clone_token": "",
@@ -22182,7 +22182,7 @@
             "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/multiplesequencealign",
             "contributors": [
                 {
@@ -38790,9 +38790,9 @@
             "url": "https://api.github.com/repos/nf-core/smrnaseq",
             "created_at": "2018-07-11T14:56:59Z",
             "updated_at": "2024-09-03T10:10:37Z",
-            "pushed_at": "2024-09-04T13:15:06Z",
+            "pushed_at": "2024-09-04T14:48:36Z",
             "homepage": "https://nf-co.re/smrnaseq",
-            "size": 8388,
+            "size": 8402,
             "stargazers_count": 72,
             "watchers_count": 72,
             "language": "Nextflow",
@@ -38805,7 +38805,7 @@
             "forks_count": 121,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 34,
+            "open_issues_count": 31,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -38815,7 +38815,7 @@
             ],
             "visibility": "public",
             "forks": 121,
-            "open_issues": 34,
+            "open_issues": 31,
             "watchers": 72,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -38903,7 +38903,7 @@
             "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/smrnaseq",
             "contributors": [
                 {
@@ -39354,8 +39354,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-09-03T14:14:56Z",
-                    "tag_sha": "ba8679150cfaacb0db8512659104f13f3e8d9748",
+                    "published_at": "2024-09-04T14:48:33Z",
+                    "tag_sha": "8a64f1968baa1b37c36c5b5d4e01e1f4a7781f30",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -39402,7 +39402,7 @@
             "updated_at": "2024-09-03T10:11:48Z",
             "pushed_at": "2024-09-04T13:41:14Z",
             "homepage": "https://nf-co.re/spatialvi",
-            "size": 7186,
+            "size": 7188,
             "stargazers_count": 48,
             "watchers_count": 48,
             "language": "Nextflow",