fix meta.yml of missing modules

modules/nf-core/affy/justrma/meta.yml

@@ -29,7 +29,7 @@ input:
         description: Path to a directory containing CEL files
         pattern: "*.{CEL,CEL.gz}"
   - - meta2:
-        ype: map
+        type: map
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test' ]

modules/nf-core/jvarkit/vcffilterjdk/meta.yml

@@ -1,4 +1,3 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "jvarkit_vcffilterjdk"
 description: Filtering VCF with dynamically-compiled java expressions
@@ -19,6 +18,7 @@ tools:
       licence: ["MIT License"]
       args_id: "$args2"
 
+      identifier: ""
   - "bcftools":
       description: |
         View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
@@ -27,91 +27,107 @@ tools:
       doi: "10.1093/bioinformatics/btp352"
       licence: ["MIT"]
       args_id: ["$args1", "$args3"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing VCF information
-        e.g. [ id:'test_reference' ]
-  - vcf:
-      type: file
-      description: Input VCF/BCF file
-      pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-  - tbi:
-      type: file
-      description: Optional VCF/BCF index file
-      pattern: "*.{tbi,csi}"
-  - regions_file:
-      type: file
-      description: Optional. Restrict to regions listed in a file
-      pattern: "*.{bed,bed.gz,txt,tsv}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing fasta information
-        e.g. [ id:'test_reference' ]
-  - fasta:
-      type: file
-      description: Fasta reference file
-      pattern: "*.fasta"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing fasta.fai information
-        e.g. [ id:'test_reference' ]
-  - fai:
-      type: file
-      description: Fasta file index
-      pattern: "*.fasta.fai"
-  - meta4:
-      type: map
-      description: |
-        Groovy Map containing fasta.dict information
-        e.g. [ id:'test_reference' ]
-  - dict:
-      type: file
-      description: GATK sequence dictionary
-      pattern: "*.dict"
-  - meta5:
-      type: map
-      description: |
-        Groovy Map containing code information
-        e.g. [ id:'test_reference' ]
-  - code:
-      type: file
-      description: File containing custom user code . May be empty if script if provided via `task.ext.args2`.
-      pattern: "*.{code,script,txt,tsv,java,js}"
-  - meta6:
-      type: map
-      description: |
-        Groovy Map containing pedigree information
-        e.g. [ id:'test_reference' ]
-  - pedigree:
-      type: file
-      description: Optional jvarkit pedigree.
-      pattern: "*.{tsv,ped,pedigree}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing VCF information
+          e.g. [ id:'test_reference' ]
+    - vcf:
+        type: file
+        description: Input VCF/BCF file
+        pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+    - tbi:
+        type: file
+        description: Optional VCF/BCF index file
+        pattern: "*.{tbi,csi}"
+    - regions_file:
+        type: file
+        description: Optional. Restrict to regions listed in a file
+        pattern: "*.{bed,bed.gz,txt,tsv}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing fasta information
+          e.g. [ id:'test_reference' ]
+    - fasta:
+        type: file
+        description: Fasta reference file
+        pattern: "*.fasta"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing fasta.fai information
+          e.g. [ id:'test_reference' ]
+    - fai:
+        type: file
+        description: Fasta file index
+        pattern: "*.fasta.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing fasta.dict information
+          e.g. [ id:'test_reference' ]
+    - dict:
+        type: file
+        description: GATK sequence dictionary
+        pattern: "*.dict"
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing code information
+          e.g. [ id:'test_reference' ]
+    - code:
+        type: file
+        description: File containing custom user code . May be empty if script if provided
+          via `task.ext.args2`.
+        pattern: "*.{code,script,txt,tsv,java,js}"
+  - - meta6:
+        type: map
+        description: |
+          Groovy Map containing pedigree information
+          e.g. [ id:'test_reference' ]
+    - pedigree:
+        type: file
+        description: Optional jvarkit pedigree.
+        pattern: "*.{tsv,ped,pedigree}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing VCF information
-        e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file
-      description: VCF filtered output file
-      pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-  - csi:
-      type: file
-      description: Default VCF file index
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing VCF information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${extension}":
+          type: file
+          description: VCF filtered output file
+          pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
   - tbi:
-      type: file
-      description: Alternative VCF file index
-      pattern: "*.tbi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing VCF information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tbi":
+          type: file
+          description: Alternative VCF file index
+          pattern: "*.tbi"
+  - csi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing VCF information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Default VCF file index
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@lindenb"
 maintainers:

modules/nf-core/multivcfanalyzer/meta.yml

@@ -20,10 +20,10 @@ tools:
       identifier: ""
 input:
   - - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
     - vcfs:
         type: file
         description: One or a list of uncompressed VCF file
@@ -79,10 +79,10 @@ input:
           Fraction of which whereby if a call falls above this value, and lower
           than the homozygous threshold, a base will be called 'heterozygous'.
   - - meta5:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
     - gff_exclude:
         type: file
         description: |

modules/nf-core/svdb/build/meta.yml

@@ -10,29 +10,35 @@ tools:
       homepage: https://github.com/J35P312/SVDB
       documentation: https://github.com/J35P312/SVDB/blob/master/README.md
       licence: ["MIT"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: Input VCF file(s) or folder
-      pattern: "*"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: Input VCF file(s) or folder
+        pattern: "*"
+  - - input_type:
+        type: string
+        description: input type
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - db:
-      type: file
-      description: SVDB database
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.db":
+          type: file
+          description: SVDB database
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@fellen31"