Merge pull request #899 from d4straub/fix-phyloseq-2.15.0dev

fix DADA2 with custom database and assignment in chunks

Author: d4straub

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#893](https://github.com/nf-core/ampliseq/pull/893),[#896](https://github.com/nf-core/ampliseq/pull/896) - Template update for nf-core/tools version 3.3.1
+- [#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.
 
 ### `Dependencies`
 

subworkflows/local/dada2_taxonomy_wf.nf

@@ -63,7 +63,7 @@ workflow DADA2_TAXONOMY_WF {
         .set { ch_fasta_chunks }
 
     //DADA2 assignTaxonomy
-    DADA2_TAXONOMY ( ch_fasta_chunks, ch_assigntax, ".${ASV_tax_name}.${val_dada_ref_taxonomy}", taxlevels )
+    DADA2_TAXONOMY ( ch_fasta_chunks, ch_assigntax.collect(), ".${ASV_tax_name}.${val_dada_ref_taxonomy}", taxlevels )
     ch_versions_dada_taxonomy = ch_versions_dada_taxonomy.mix(DADA2_TAXONOMY.out.versions)
 
     // collect all DADA2_TAXONOMY.out.tsv into one file
@@ -79,7 +79,7 @@ workflow DADA2_TAXONOMY_WF {
 
     //DADA2 addSpecies
     if (!params.skip_dada_addspecies) {
-        DADA2_ADDSPECIES ( DADA2_TAXONOMY.out.rds, ch_addspecies, taxlevels )
+        DADA2_ADDSPECIES ( DADA2_TAXONOMY.out.rds, ch_addspecies.collect(), taxlevels )
 
         // collect all DADA2_ADDSPECIES.out.tsv into one file
         DADA2_ADDSPECIES.out.tsv