Reformat & Update meta.yml

Author: dhtt

subworkflows/nf-core/vcf_vembrane/main.nf

@@ -1,9 +1,7 @@
-include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX   } from '../../../modules/nf-core/tabix/bgziptabix/main'
+include { TABIX_BGZIPTABIX                       } from '../../../modules/nf-core/tabix/bgziptabix/main'
 include { VEMBRANE_FILTER                        } from '../../../modules/nf-core/vembrane/filter/main'
-include {
-    VEMBRANE_SORT as VEMBRANE_SORT_DEFAULT ;
-    VEMBRANE_SORT as VEMBRANE_SORT_VCF
-} from '../../../modules/nf-core/vembrane/sort/main'
+include { VEMBRANE_SORT as VEMBRANE_SORT_DEFAULT } from '../../../modules/nf-core/vembrane/sort/main'
+include { VEMBRANE_SORT as VEMBRANE_SORT_VCF     } from '../../../modules/nf-core/vembrane/sort/main'
 include { VEMBRANE_TABLE                         } from '../../../modules/nf-core/vembrane/table/main'
 
 workflow VCF_VEMBRANE {
@@ -36,10 +34,10 @@ workflow VCF_VEMBRANE {
     // Always sort by 'CHROM, POS' before index and output compression
     VEMBRANE_SORT_DEFAULT(ch_vcf_current, "CHROM, POS")
     ch_vcf_current = VEMBRANE_SORT_DEFAULT.out.vcf
+    ch_versions = ch_versions.mix(VEMBRANE_SORT_DEFAULT.out.versions)
 
     // Index VCF.GZ (always performed on final VCF)
     TABIX_BGZIPTABIX(ch_vcf_current)
-    filtered_ch = TABIX_BGZIPTABIX.out.gz_tbi
     ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
 
     // Conditionally create TSV table
@@ -52,9 +50,11 @@ workflow VCF_VEMBRANE {
         // Create empty channel when table is not generated
         tsv_ch = Channel.empty()
     }
+    ch_vcf = TABIX_BGZIPTABIX.out.gz_tbi
 
     emit:
-    filtered_ch               // channel: [ meta, path(vcf_file), path(tbi_file) ]
-    tsv_ch                    // channel: [ meta, path(table_file) ] or empty
-    versions    = ch_versions // channel: [ path(versions.yml) ]
+    vcf      = ch_vcf_current // channel: [ val(meta), path(vcf_file), path(tbi_file) ]
+    tsv      = tsv_ch         // channel: [ val(meta), path(table_file) ] or empty
+
+    versions = ch_versions    // channel: [ path(versions.yml) ]
 }

subworkflows/nf-core/vcf_vembrane/meta.yml

@@ -3,11 +3,10 @@ name: "vcf_vembrane"
 description: Filter and/or sort and optionally produce a TSV table for a VCF with vembrane.
 keywords:
   - vcf
-  - variant
   - filtering
   - sorting
+  - indexing
   - vembrane
-  - bgzip
   - tabix
   - table
   - tsv
@@ -18,41 +17,38 @@ components:
   - tabix/bgziptabix
 input:
   - ch_vcf:
-      type: tuple
+      type: channel
       description: |
-        Input channel containing metadata and a VCF/BCF file to process.
-        Structure: [ val(meta), path(vcf) ]
+        Channel containing sample metadata and VCF files
+        Structure: [ meta, vcf ]
   - filter_expression:
-      type: val
-      description: |
-        Vembrane filter expression to select variants.
-        If empty or 'null', the filtering step is skipped.
+      type: string
+      description: Expression for vembrane filter (optional - can be empty string or null)
+      required: false
   - sort_expression:
-      type: val
-      description: |
-        Vembrane sort expression used for optional intermediate sorting.
-        If empty or 'null', this step is skipped.
-        A final CHROM,POS sort is always applied.
+      type: string
+      description: Expression for vembrane sort (optional - can be empty string or null)
+      required: false
   - table_expression:
-      type: val
-      description: |
-        Vembrane table expression to generate a TSV table.
-        If empty or 'null', table generation is skipped.
+      type: string
+      description: Expression for vembrane table generation (optional - can be empty string or null)
+      required: false
 output:
-  - filtered_ch:
-      type: file
+  - vcf:
+      type: channel
       description: |
-        Final filtered and sorted VCF file, bgzipped and indexed with Tabix.
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
-  - tsv_ch:
-      type: file
+        Processed and sorted VCF files
+        Structure: [ meta, vcf, tbi ]
+      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz,.tbi}"
+  - tsv:
+      type: channel
       description: |
-        Optional vembrane table (TSV) generated if a table expression is provided.
-      pattern: "*.{tsv}"
+        TSV table files generated from VCF (empty channel if table_expression not provided)
+        Structure: [ meta, tsv ]
+      pattern: "*.tsv"
   - versions:
       type: file
-      description: |
-        File containing software version information aggregated from all components.
+      description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@dhtt"