export phyloseq and tse by default

nf-core · Nov 26, 2024 · bd7a1ff · bd7a1ff
1 parent cf4eeba
commit bd7a1ff
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Showing 4 changed files with 17 additions and 29 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -82,8 +82,6 @@ params {
     ancombc_significance       = 0.05
     ancombc_formula            = null
     ancombc_formula_reflvl     = null
-    phyloseq                   = false
-    treesummarizedexperiment   = false
 
     // Report options
     report_template   = "${projectDir}/assets/report_template.Rmd"
@@ -107,6 +105,8 @@ params {
     skip_dada_addspecies   = false
     skip_alpha_rarefaction = false
     skip_diversity_indices = false
+    skip_phyloseq          = false
+    skip_tse               = false
     skip_multiqc           = false
     skip_report            = false
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -732,23 +732,6 @@
             },
             "fa_icon": "fas fa-book-open"
         },
-        "exporting_results": {
-            "title": "Exporting objects for downstream analysis",
-            "type": "object",
-            "description": "Opt-in to create R objects",
-            "default": "",
-            "properties": {
-                "phyloseq": {
-                    "type": "boolean",
-                    "description": "Export phyloseq rds object(s)"
-                },
-                "treesummarizedexperiment": {
-                    "type": "boolean",
-                    "description": "Export TreeSummarizedExperiment rds object(s)"
-                }
-            },
-            "fa_icon": "fas fa-book-open"
-        },
         "skipping_specific_steps": {
             "title": "Skipping specific steps",
             "type": "object",
@@ -807,6 +790,14 @@
                     "type": "boolean",
                     "description": "Skip alpha and beta diversity analysis"
                 },
+                "skip_phyloseq": {
+                    "type": "boolean",
+                    "description": "Skip exporting phyloseq rds object(s)"
+                },
+                "skip_tse": {
+                    "type": "boolean",
+                    "description": "Skip exporting TreeSummarizedExperiment rds object(s)"
+                },
                 "skip_multiqc": {
                     "type": "boolean",
                     "description": "Skip MultiQC reporting"
@@ -1006,9 +997,6 @@
         {
             "$ref": "#/$defs/pipeline_report"
         },
-        {
-            "$ref": "#/$defs/exporting_results"
-        },
         {
             "$ref": "#/$defs/skipping_specific_steps"
         },

diff --git a/subworkflows/local/robject_workflow.nf b/subworkflows/local/robject_workflow.nf
@@ -39,18 +39,18 @@ workflow ROBJECT_WORKFLOW {
         ch_robject_inasv = ch_tsv
     }
 
-    if ( params.phyloseq ) {
+    if ( !params.skip_phyloseq ) {
         PHYLOSEQ ( ch_tax.combine(ch_robject_inasv), ch_robject_inmeta, ch_robject_intree )
         ch_versions_robject_workflow = ch_versions_robject_workflow.mix(PHYLOSEQ.out.versions)
     }
 
-    if ( params.treesummarizedexperiment ) {
+    if ( !params.skip_tse ) {
         TREESUMMARIZEDEXPERIMENT ( ch_tax.combine(ch_robject_inasv), ch_robject_inmeta, ch_robject_intree )
         ch_versions_robject_workflow = ch_versions_robject_workflow.mix(TREESUMMARIZEDEXPERIMENT.out.versions)
     }
 
     emit:
-    phyloseq                 = params.phyloseq ? PHYLOSEQ.out.rds : []
-    treesummarizedexperiment = params.treesummarizedexperiment ? TREESUMMARIZEDEXPERIMENT.out.rds : []
-    versions                 = ch_versions_robject_workflow
+    phyloseq = !params.skip_phyloseq ? PHYLOSEQ.out.rds : []
+    tse      = !params.skip_tse ? TREESUMMARIZEDEXPERIMENT.out.rds : []
+    versions = ch_versions_robject_workflow
 }
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -868,7 +868,7 @@ workflow AMPLISEQ {
     //
     // SUBWORKFLOW: Create R objects
     //
-    if ( !params.skip_taxonomy && ( params.phyloseq || params.treesummarizedexperiment ) ) {
+    if ( !params.skip_taxonomy && ( !params.skip_phyloseq || !params.skip_tse ) ) {
         if ( params.pplace_tree ) {
             ch_tree_for_robject = FASTA_NEWICK_EPANG_GAPPA.out.grafted_phylogeny
         } else {
@@ -1012,7 +1012,7 @@ workflow AMPLISEQ {
             run_qiime2 && params.ancombc_formula && params.metadata ? QIIME2_ANCOM.out.ancombc_formula.collect().ifEmpty( [] ) : [],
             params.picrust ? PICRUST.out.pathways.ifEmpty( [] ) : [],
             params.sbdiexport ? SBDIEXPORT.out.sbditables.mix(SBDIEXPORTREANNOTATE.out.sbdiannottables).collect().ifEmpty( [] ) : [],
-            !params.skip_taxonomy && params.phyloseq ? ROBJECT_WORKFLOW.out.phyloseq.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : []
+            !params.skip_taxonomy && !params.skip_phyloseq ? ROBJECT_WORKFLOW.out.phyloseq.map{info,rds -> [rds]}.collect().ifEmpty( [] ) : []
             //TODO: add treesummarizedexperiment
         )
         ch_versions    = ch_versions.mix(SUMMARY_REPORT.out.versions)