Make addSpecies optional also when using cut_its

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+* [#](https://github.com/nf-core/ampliseq/pull/) - Make `--skip_dada_addspecies` compatible with `--cut_its`
 * [#352](https://github.com/nf-core/ampliseq/pull/352) - `--skip_dada_addspecies` allows to skip species level classification to reduce memory requirements, incompatible with `--sbdiexport` and `--cut_its` that expect species annotation
 * [#354](https://github.com/nf-core/ampliseq/pull/354) - Input files and files after primer trimming with cutadapt are required to be >1KB (i.e. not empty) and either the pipeline will stop if at least one sample file fails or the failing samples will be ignored when using `--ignore_empty_input_files` or `--ignore_failed_trimming`, respectively.
 * [#364](https://github.com/nf-core/ampliseq/pull/364) - Adonis in QIIME2 for testing feature importance in beta diversity distances, `--qiime_adonis_formula` can be set to provide a custom formula.

lib/WorkflowAmpliseq.groovy

@@ -38,10 +38,6 @@ class WorkflowAmpliseq {
             System.exit(1)
         }
 
-        if (params.skip_dada_addspecies && params.cut_its) {
-            log.error "Incompatible parameters: `--cut_its` expects species annotation and therefore excludes `--skip_dada_addspecies`."
-            System.exit(1)
-        }
     }
 
     //

modules/local/format_taxresults.nf

@@ -8,16 +8,14 @@ process FORMAT_TAXRESULTS {
 
     input:
     path(taxtable)
-    path(taxtable_species)
     path(fastafile)
+    val(outfile)
 
     output:
-    path("ASV_tax.tsv")
-    path("ASV_tax_species.tsv"), emit: tsv
+    path(outfile), emit: tsv
 
     script:
     """
     add_full_sequence_to_taxfile.py $taxtable $fastafile
-    add_full_sequence_to_taxfile.py $taxtable_species $fastafile
     """
 }

nextflow_schema.json

@@ -342,7 +342,7 @@
                 },
                 "skip_dada_addspecies": {
                     "type": "boolean",
-                    "description": "Skip species level when using DADA2 for taxonomic classification, that reduces required memory dramatically under certain conditions. Incompatible with `--sbdiexport` and `--cut_its`"
+                    "description": "Skip species level when using DADA2 for taxonomic classification, that reduces required memory dramatically under certain conditions. Incompatible with `--sbdiexport`"
                 },
                 "skip_barplot": {
                     "type": "boolean",

workflows/ampliseq.nf

@@ -97,6 +97,7 @@ include { MERGE_STATS                   } from '../modules/local/merge_stats'
 include { DADA2_TAXONOMY                } from '../modules/local/dada2_taxonomy'
 include { DADA2_ADDSPECIES              } from '../modules/local/dada2_addspecies'
 include { FORMAT_TAXRESULTS             } from '../modules/local/format_taxresults'
+include { FORMAT_TAXRESULTS as FORMAT_TAXRESULTS_ADDSP } from '../modules/local/format_taxresults'
 include { QIIME2_INSEQ                  } from '../modules/local/qiime2_inseq'
 include { QIIME2_FILTERTAXA             } from '../modules/local/qiime2_filtertaxa'
 include { QIIME2_INASV                  } from '../modules/local/qiime2_inasv'
@@ -328,9 +329,14 @@ workflow AMPLISEQ {
             ch_versions = ch_versions.mix(ITSX_CUTASV.out.versions.ifEmpty(null))
             ch_cut_fasta = ITSX_CUTASV.out.fasta
             DADA2_TAXONOMY ( ch_cut_fasta, ch_assigntax, 'ASV_ITS_tax.tsv' )
-            DADA2_ADDSPECIES ( DADA2_TAXONOMY.out.rds, ch_addspecies, 'ASV_ITS_tax_species.tsv' )
-            FORMAT_TAXRESULTS ( DADA2_TAXONOMY.out.tsv, DADA2_ADDSPECIES.out.tsv, ch_fasta )
-            ch_dada2_tax = FORMAT_TAXRESULTS.out.tsv
+            FORMAT_TAXRESULTS ( DADA2_TAXONOMY.out.tsv, ch_fasta, 'ASV_tax.tsv' )
+            if (!params.skip_dada_addspecies) {
+                DADA2_ADDSPECIES ( DADA2_TAXONOMY.out.rds, ch_addspecies, 'ASV_ITS_tax_species.tsv' )
+                FORMAT_TAXRESULTS_ADDSP ( DADA2_ADDSPECIES.out.tsv, ch_fasta, 'ASV_tax_species.tsv' )
+                ch_dada2_tax = FORMAT_TAXRESULTS_ADDSP.out.tsv
+            } else {
+                ch_dada2_tax = FORMAT_TAXRESULTS.out.tsv
+            }
         }
     }