Sync coverm/contig module and update binning subworkflow

- Sync coverm/contig main.nf and meta.yml to reference (eval/topic
  versioning, List-aware methods string handling)
- Remove ch_versions.mix for COVERM_CONTIG calls (topic versioning
  is automatic; no versions.yml emitted)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: vinisalazar

modules/nf-core/coverm/contig/main.nf

@@ -61,7 +61,6 @@ workflow BINNING {
                 reference: [meta, []]
             }
         COVERM_CONTIG_LONGREAD(ch_longread_depth.reads, ch_longread_depth.reference, true, false, params.coverm_methods)
-        ch_versions = ch_versions.mix(COVERM_CONTIG_LONGREAD.out.versions)
         ch_longread_contig_depths = COVERM_CONTIG_LONGREAD.out.coverage
     }
     else {
@@ -91,7 +90,6 @@ workflow BINNING {
                 }
             COVERM_CONTIG_SHORTREAD(ch_shortread_depth.reads, ch_shortread_depth.reference, false, false, params.coverm_methods)
         }
-        ch_versions = ch_versions.mix(COVERM_CONTIG_SHORTREAD.out.versions)
         ch_shortread_contig_depths = COVERM_CONTIG_SHORTREAD.out.coverage
     }
     else {