From 849b6efcc3380335f0952acaf8da630a651035cb Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Mon, 6 Nov 2023 10:27:08 +0000
Subject: [PATCH] update nextflow workflow with latest phylo changes

---
 main.nf              |  6 ++----
 nextflow.config      |  7 +++----
 nextflow_schema.json | 12 +++---------
 3 files changed, 8 insertions(+), 17 deletions(-)

diff --git a/main.nf b/main.nf
index 27ffb0b..db74dc3 100644
--- a/main.nf
+++ b/main.nf
@@ -31,10 +31,8 @@ process run_piranha {
         extra += " --primer-length ${params.primer_length}"
     if ( params.run_phylo )
         extra += " --run-phylo"
-    if ( params.supplementary_sequences )
-        extra += " --supplementary-sequences ${params.supplementary_sequences}"
-    if ( params.supplementary_metadata )
-        extra += " --supplementary-metadata ${params.supplementary_metadata}"
+    if ( params.supplementary_datadir )
+        extra += " --supplementary-datadir ${params.supplementary_datadir}"
     """
     piranha -b ${barcodes_csv} -i ${run_dir} -o piranha_output --tempdir piranha_tmp -t ${task.cpus} ${extra}
     mv piranha_output/report.html piranha_output/piranha_report.html
diff --git a/nextflow.config b/nextflow.config
index 8d2eec3..f0598be 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,8 +32,7 @@ params {
 
     // Phylo options
     run_phylo = false
-    supplementary_sequences = null
-    supplementary_metadata = null
+    supplementary_datadir = null
 
     // Other options
     disable_ping = false
@@ -64,7 +63,7 @@ manifest {
     description     = 'Polio investigation resource automating nanopore haplotype analysis.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = '1.1.2'
+    version         = '1.2'
 }
 
 
@@ -129,4 +128,4 @@ trace {
 
 env {
 	PYTHONNOUSERSITE = 1
-}
\ No newline at end of file
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 991986b..7949920 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -105,17 +105,11 @@
           "type": "boolean",
           "title": "Run phylogenetics pipeline"
         },
-        "supplementary_sequences": {
+        "supplementary_datadir": {
           "type": "string",
           "format": "path",
-          "title": "Supplementary sequences",
-          "description": "Supplementary sequence FASTA file to be incorporated into phylogenetic analysis"
-        },
-        "supplementary_metadata": {
-          "type": "string",
-          "format": "path",
-          "title": "Supplementary metadata",
-          "description": " Supplementary metadata file associated with the supplementary sequence FASTA file"
+          "title": "Supplementary data",
+          "description": "Path to directory containing supplementary sequence FASTA file and optional metadata to be incorporated into phylogenetic analysis."
         }
       }
     },