Merge branch 'main' of https://github.com/aineniamh/piranha into main

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

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
-}
+}

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."
         }
       }
     },