From b81f26298d2f983cf62944e8609f947ff292c06d Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Wed, 24 Jul 2024 20:47:35 -0300
Subject: [PATCH] feat: Add build upset to annotation subwf

---
 nextflow.config                  |  1 +
 nextflow_schema.json             |  7 ++++++-
 subworkflows/local/annotation.nf | 10 ++++++++++
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index fcabd78..821661c 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -37,6 +37,7 @@ params {
     annotation_tools           = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy,report'
     feature_profile_columns    = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet'
     feature_dispersion_columns = null
+    upset_plot_columns         = null
     min_pident                 = 60
     min_qcover                 = 0.6
     skip_profile_creation      = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 73d9df3..6e3a975 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -148,6 +148,11 @@
                     "fa_icon": "fas fa-columns",
                     "description": "Columns to include in the feature profile",
                     "pattern": "^((rgi|mobsuite|vfdb|cazy|bacmet|iceberg)?,?)*(?<!,)$"
+                },
+                "upset_plot_columns": {
+                    "type": "string",
+                    "fa_icon": "fas fa-columns",
+                    "description": "Columns to use for making Upset plots of genome features"
                 }
             }
         },
@@ -215,7 +220,7 @@
                 },
                 "core_similarity": {
                     "type": "number",
-                    "default": 99.99,
+                    "default": 99.9,
                     "fa_icon": "fas fa-clone",
                     "description": "Similarity threshold for core genomes"
                 },
diff --git a/subworkflows/local/annotation.nf b/subworkflows/local/annotation.nf
index c0d9d69..1d8942a 100755
--- a/subworkflows/local/annotation.nf
+++ b/subworkflows/local/annotation.nf
@@ -35,6 +35,7 @@ include { CONCAT_OUTPUT as CONCAT_MOBSUITE;
           CONCAT_OUTPUT as CONCAT_INTEGRONS } from '../../modules/local/concat_output.nf'
 include { FILTER_AND_CONCAT_MATCHES as FILTER_RGI } from '../../modules/local/filter_matches'
 include { CREATE_REPORT } from '../../modules/local/create_report'
+include { BUILD_UPSET } from '../../modules/local/build_upset/main'
 
 //
 // SUBWORKFLOWS
@@ -356,6 +357,15 @@ workflow ANNOTATE_ASSEMBLIES {
             profile = (params.skip_profile_creation) ? profile : CREATE_REPORT.out.profile
         }
 
+        if (params.upset_plot_columns) {
+            BUILD_UPSET(
+                profile,
+                file(params.input_sample_table),
+                params.upset_plot_columns
+            )
+        }
+
+
     emit:
         annotation = concat_annotation
         annotation_software = ch_software_versions