allow QIIME2 with conda and custom database

d4straub · d4straub · commit 43926b4b9ab3 · 2025-09-19T16:15:28.000+02:00
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -232,7 +232,7 @@ workflow AMPLISEQ {
     }
 
     // Only run QIIME2 taxonomy classification if needed parameters are passed and we are not skipping taxonomy or qiime steps.
-    if ( !(workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) && !params.skip_taxonomy && !params.skip_qiime && (params.qiime_ref_taxonomy || params.qiime_ref_tax_custom || params.classifier) ) {
+    if ( !params.skip_taxonomy && !params.skip_qiime && (params.qiime_ref_taxonomy || params.qiime_ref_tax_custom || params.classifier) ) {
         run_qiime2_taxonomy = true
     } else {
         run_qiime2_taxonomy = false

Original file line number	Diff line number	Diff line change
`@@ -232,7 +232,7 @@ workflow AMPLISEQ {`
`232`	`232`	`}`
`233`	`233`
`234`	`234`	`// Only run QIIME2 taxonomy classification if needed parameters are passed and we are not skipping taxonomy or qiime steps.`
`235`		`- if ( !(workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) && !params.skip_taxonomy && !params.skip_qiime && (params.qiime_ref_taxonomy \|\| params.qiime_ref_tax_custom \|\| params.classifier) ) {`
	`235`	`+ if ( !params.skip_taxonomy && !params.skip_qiime && (params.qiime_ref_taxonomy \|\| params.qiime_ref_tax_custom \|\| params.classifier) ) {`
`236`	`236`	`run_qiime2_taxonomy = true`
`237`	`237`	`} else {`
`238`	`238`	`run_qiime2_taxonomy = false`