Make sure downstream is aware of new means of pointing to a qiime ref…

… db.
nf-core · Nov 29, 2023 · 1d6ce32 · 1d6ce32
1 parent 7907df5
commit 1d6ce32
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -624,7 +624,7 @@ workflow AMPLISEQ {
             log.info "Use Kraken2 taxonomy classification"
             val_used_taxonomy = "Kraken2"
             ch_tax = QIIME2_INTAX ( ch_kraken2_tax, "" ).qza
-        } else if ( params.qiime_ref_taxonomy || params.classifier ) {
+        } else if ( params.qiime_ref_taxonomy || params.qiime_ref_tax_custom || params.classifier ) {
             log.info "Use QIIME2 taxonomy classification"
             val_used_taxonomy = "QIIME2"
             ch_tax = QIIME2_TAXONOMY.out.qza
@@ -724,7 +724,7 @@ workflow AMPLISEQ {
     // MODULE: Predict functional potential of a bacterial community from marker genes with Picrust2
     //
     if ( params.picrust ) {
-        if ( run_qiime2 && !params.skip_abundance_tables && ( params.dada_ref_taxonomy || params.qiime_ref_taxonomy || params.classifier || params.sintax_ref_taxonomy || params.kraken2_ref_taxonomy || params.kraken2_ref_tax_custom ) && !params.skip_taxonomy ) {
+        if ( run_qiime2 && !params.skip_abundance_tables && ( params.dada_ref_taxonomy || params.qiime_ref_taxonomy || params.qiime_ref_tax_custom || params.classifier || params.sintax_ref_taxonomy || params.kraken2_ref_taxonomy || params.kraken2_ref_tax_custom ) && !params.skip_taxonomy ) {
             PICRUST ( QIIME2_EXPORT.out.abs_fasta, QIIME2_EXPORT.out.abs_tsv, "QIIME2", "This Picrust2 analysis is based on filtered reads from QIIME2" )
         } else {
             PICRUST ( ch_fasta, ch_dada2_asv, "DADA2", "This Picrust2 analysis is based on unfiltered reads from DADA2" )
@@ -856,7 +856,7 @@ workflow AMPLISEQ {
             !params.skip_taxonomy && ( params.kraken2_ref_taxonomy || params.kraken2_ref_tax_custom ) ? KRAKEN2_TAXONOMY_WF.out.tax_tsv.ifEmpty( [] ) : [],
             !params.skip_taxonomy && params.pplace_tree ? ch_pplace_tax.ifEmpty( [] ) : [],
             !params.skip_taxonomy && params.pplace_tree ? FASTA_NEWICK_EPANG_GAPPA.out.heattree.ifEmpty( [[],[]] ) : [[],[]],
-            !params.skip_taxonomy && ( params.qiime_ref_taxonomy || params.classifier ) && run_qiime2 ? QIIME2_TAXONOMY.out.tsv.ifEmpty( [] ) : [],
+            !params.skip_taxonomy && ( params.qiime_ref_taxonomy || params.qiime_ref_tax_custom || params.classifier ) && run_qiime2 ? QIIME2_TAXONOMY.out.tsv.ifEmpty( [] ) : [],
             run_qiime2,
             run_qiime2 ? val_used_taxonomy : "",
             run_qiime2 && ( params.exclude_taxa != "none" || params.min_frequency != 1 || params.min_samples != 1 ) ? ch_dada2_asv.countLines()+","+QIIME2_FILTERTAXA.out.tsv.countLines() : "",