[automated] Update json files and markdown cache

nf-core · Oct 7, 2024 · b680514 · b680514
1 parent 0628750
commit b680514
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Showing 3 changed files with 120 additions and 91 deletions.
diff --git a/.cache.tar.xz b/.cache.tar.xz
diff --git a/public/components.json b/public/components.json
@@ -7636,6 +7636,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -24988,6 +24992,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -106554,6 +106566,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -114235,11 +114251,11 @@
             "versions": [
               {
                 "versions.yml": {
-                "type": "file",
-                "description": "File containing software versions",
-                "pattern": "versions.yml"
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
                 }
-            }
+              }
             ]
           }
         ],
@@ -167037,14 +167053,24 @@
                 }
               },
               {
-                "*sortedByCoord.out.bam": {
+                "${prefix}.sortedByCoord.out.bam": {
                   "type": "file",
                   "description": "Sorted BAM file of read alignments (optional)",
                   "pattern": "*sortedByCoord.out.bam"
                 }
               }
             ]
           },
+          {
+            "bam_sorted_aligned": [
+              {
+                "meta": {}
+              },
+              {
+                "${prefix}.Aligned.sortedByCoord.out.bam": {}
+              }
+            ]
+          },
           {
             "bam_transcript": [
               {
@@ -167122,13 +167148,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.SJ.out.tab"
                 }
               },
               {
                 "*.SJ.out.tab": {
-                  "type": "file",
-                  "description": "STAR output splice junction tab file",
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.SJ.out.tab"
                 }
               }
@@ -167139,13 +167166,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.ReadsPerGene.out.tab"
                 }
               },
               {
                 "*.ReadsPerGene.out.tab": {
-                  "type": "file",
-                  "description": "STAR output read per gene tab file",
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.ReadsPerGene.out.tab"
                 }
               }
@@ -167174,13 +167202,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.out.sam"
                 }
               },
               {
                 "*.out.sam": {
-                  "type": "file",
-                  "description": "STAR output SAM file",
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.out.sam"
                 }
               }
@@ -198254,4 +198283,4 @@
       }
     }
   ]
-}
+}