Merge pull request #906 from nhenry50/fix-consensus-merge-pair-single-sample-run

fix consensus merge pairs with one sample run

Author: nhenry50

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#906](https://github.com/nf-core/ampliseq/pull/906) - Fix `--mergepairs_strategy "consensus"` causing an error in dada2_stats when analysing a run composed by only one sample
 - [#893](https://github.com/nf-core/ampliseq/pull/893),[#896](https://github.com/nf-core/ampliseq/pull/896),[#905](https://github.com/nf-core/ampliseq/pull/905) - Template update for nf-core/tools version 3.3.2
 - [#897](https://github.com/nf-core/ampliseq/pull/897) - Allow multiple region analysis with one sample
 - [#899](https://github.com/nf-core/ampliseq/pull/899) - With `--dada_ref_tax_custom` all chunks defined by `--dada_assign_chunksize` are now taxonomically annotated.

modules/local/dada2_denoising.nf

@@ -90,6 +90,12 @@ process DADA2_DENOISING {
 
             }
 
+            # if one sample, need to convert back to df for next steps
+
+            if(length(mergers) == 1) {
+                mergers <- mergers[[1]]
+            }
+
         } else {
             mergers <- mergePairs(dadaFs, filtFs, dadaRs, filtRs, $args2, verbose=TRUE)
         }