[automated] Update json files and markdown cache

nf-core · Feb 10, 2024 · 6202e7c · 6202e7c
1 parent 499746f
commit 6202e7c
Show file tree

Hide file tree

Showing 3 changed files with 201 additions and 35 deletions.
diff --git a/.cache.tar.xz b/.cache.tar.xz
diff --git a/public/components.json b/public/components.json
@@ -4002,6 +4002,10 @@
           "name": "rnafusion",
           "version": "3.0.1"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.1"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.1"
@@ -37393,6 +37397,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -38822,6 +38830,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -43403,6 +43415,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -87858,6 +87874,137 @@
         }
       ]
     },
+    {
+      "name": "quartonotebook",
+      "path": "modules/nf-core/quartonotebook/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "quartonotebook",
+        "description": "Render a Quarto notebook, including parametrization.",
+        "keywords": [
+          "quarto",
+          "notebook",
+          "reports",
+          "python",
+          "r"
+        ],
+        "tools": [
+          {
+            "quartonotebook": {
+              "description": "An open-source scientific and technical publishing system.",
+              "homepage": "https://quarto.org/",
+              "documentation": "https://quarto.org/docs/reference/",
+              "tool_dev_url": "https://github.com/quarto-dev/quarto-cli",
+              "licence": [
+                "MIT"
+              ]
+            }
+          },
+          {
+            "papermill": {
+              "description": "Parameterize, execute, and analyze notebooks",
+              "homepage": "https://github.com/nteract/papermill",
+              "documentation": "http://papermill.readthedocs.io/en/latest/",
+              "tool_dev_url": "https://github.com/nteract/papermill",
+              "licence": [
+                "BSD 3-clause"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n"
+            }
+          },
+          {
+            "notebook": {
+              "type": "file",
+              "description": "The Quarto notebook to be rendered.",
+              "pattern": "*.{qmd}"
+            }
+          },
+          {
+            "parameters": {
+              "type": "map",
+              "description": "Groovy map with notebook parameters which will be passed to Quarto to\ngenerate parametrized reports.\n"
+            }
+          },
+          {
+            "input_files": {
+              "type": "file",
+              "description": "One or multiple files serving as input data for the notebook.",
+              "pattern": "*"
+            }
+          },
+          {
+            "extensions": {
+              "type": "file",
+              "description": "A quarto `_extensions` directory with custom template(s) to be\navailable for rendering.\n",
+              "pattern": "*"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`.\n"
+            }
+          },
+          {
+            "html": {
+              "type": "file",
+              "description": "HTML report generated by Quarto.",
+              "pattern": "*.html"
+            }
+          },
+          {
+            "notebook": {
+              "type": "file",
+              "description": "The original, un-rendered notebook.",
+              "pattern": "*.[qmd,ipynb,rmd]"
+            }
+          },
+          {
+            "artifacts": {
+              "type": "file",
+              "description": "Artifacts generated during report rendering.",
+              "pattern": "*"
+            }
+          },
+          {
+            "params_yaml": {
+              "type": "file",
+              "description": "Parameters used during report rendering.",
+              "pattern": "*"
+            }
+          },
+          {
+            "extensions": {
+              "type": "file",
+              "description": "Quarto extensions used during report rendering.",
+              "pattern": "*"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions.",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@fasterius"
+        ],
+        "maintainers": [
+          "@fasterius"
+        ]
+      }
+    },
     {
       "name": "quast",
       "path": "modules/nf-core/quast/meta.yml",
@@ -122454,6 +122601,10 @@
           "name": "fetchngs",
           "version": "1.11.0"
         },
+        {
+          "name": "fetchngs",
+          "version": "1.11.0"
+        },
         {
           "name": "fetchngs",
           "version": "1.11.0"
@@ -123299,6 +123450,10 @@
           "name": "fetchngs",
           "version": "1.11.0"
         },
+        {
+          "name": "fetchngs",
+          "version": "1.11.0"
+        },
         {
           "name": "fetchngs",
           "version": "1.11.0"
@@ -124177,6 +124332,10 @@
           "name": "fetchngs",
           "version": "1.11.0"
         },
+        {
+          "name": "fetchngs",
+          "version": "1.11.0"
+        },
         {
           "name": "fetchngs",
           "version": "1.11.0"
@@ -124442,7 +124601,14 @@
           "version"
         ],
         "components": [],
-        "input": [],
+        "input": [
+          {
+            "nextflow_cli_args": {
+              "type": "list",
+              "description": "Nextflow CLI positional arguments\n"
+            }
+          }
+        ],
         "output": [
           {
             "success": {