Merge pull request #2787 from mashehu/fix-modules

update components.json
nf-core · Oct 11, 2024 · c2296d7 · c2296d7
2 parents dca1319 + f659497
commit c2296d7
Showing 1 changed file with 57 additions and 48 deletions.
diff --git a/public/components.json b/public/components.json
@@ -7684,6 +7684,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -25139,6 +25143,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -106885,6 +106897,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -167365,9 +167381,8 @@
             "log_final": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR final log file",
-                  "pattern": "*Log.final.out"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167383,9 +167398,8 @@
             "log_out": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR lot out file",
-                  "pattern": "*Log.out"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167401,9 +167415,8 @@
             "log_progress": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR log progress file",
-                  "pattern": "*Log.progress.out"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167430,9 +167443,8 @@
             "bam": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "Output BAM file containing read alignments",
-                  "pattern": "*.{bam}"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167448,9 +167460,8 @@
             "bam_sorted": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "Sorted BAM file of read alignments (optional)",
-                  "pattern": "*sortedByCoord.out.bam"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167465,20 +167476,26 @@
           {
             "bam_sorted_aligned": [
               {
-                "meta": {}
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                }
               },
               {
-                "${prefix}.Aligned.sortedByCoord.out.bam": {}
+                "${prefix}.Aligned.sortedByCoord.out.bam": {
+                  "type": "file",
+                  "description": "Sorted BAM file of read alignments (optional)",
+                  "pattern": "*.Aligned.sortedByCoord.out.bam"
+                }
               }
             ]
           },
           {
             "bam_transcript": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "Output BAM file of transcriptome alignment (optional)",
-                  "pattern": "*toTranscriptome.out.bam"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167494,9 +167511,8 @@
             "bam_unsorted": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "Unsorted BAM file of read alignments (optional)",
-                  "pattern": "*Aligned.unsort.out.bam"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167512,9 +167528,8 @@
             "fastq": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "Unmapped FastQ files (optional)",
-                  "pattern": "*fastq.gz"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167530,9 +167545,8 @@
             "tab": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR output tab file(s) (optional)",
-                  "pattern": "*.tab"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167549,14 +167563,13 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
-                  "pattern": "*.SJ.out.tab"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
                 "*.SJ.out.tab": {
-                  "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "type": "file",
+                  "description": "STAR output splice junction tab file",
                   "pattern": "*.SJ.out.tab"
                 }
               }
@@ -167567,14 +167580,13 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
-                  "pattern": "*.ReadsPerGene.out.tab"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
                 "*.ReadsPerGene.out.tab": {
-                  "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "type": "file",
+                  "description": "STAR output read per gene tab file",
                   "pattern": "*.ReadsPerGene.out.tab"
                 }
               }
@@ -167584,9 +167596,8 @@
             "junction": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR chimeric junction output file (optional)",
-                  "pattern": "*.out.junction"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167609,8 +167620,8 @@
               },
               {
                 "*.out.sam": {
-                  "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "type": "file",
+                  "description": "STAR output SAM file(s) (optional)",
                   "pattern": "*.out.sam"
                 }
               }
@@ -167620,9 +167631,8 @@
             "wig": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR output wiggle format file(s) (optional)",
-                  "pattern": "*.wig"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {
@@ -167638,9 +167648,8 @@
             "bedgraph": [
               {
                 "meta": {
-                  "type": "file",
-                  "description": "STAR output bedGraph format file(s) (optional)",
-                  "pattern": "*.bg"
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
                 }
               },
               {