Merge branch 'cw-1360-change-sample_sheet-format-to-file-path' into '…

…dev'

set sample sheet format in schema to "file-path"

See merge request epi2melabs/workflows/wf-bacterial-genomes!52

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.2.10]
+### Fixed
+- sample_sheet format in schema to expect a file
+
 ## [v0.2.9]
 ### Changed
 - Updated description in manifest

nextflow.config

@@ -13,7 +13,7 @@ params {
     chunk_size = 1000000
     run_prokka = true
     prokka_opts = null
-    wfversion = "v0.2.9"
+    wfversion = "v0.2.10"
     aws_image_prefix = null
     aws_queue = null
     sample = null
@@ -47,7 +47,7 @@ manifest {
     description     = 'Assembly, variant calling, and annotation of bacterial genomes.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v0.2.9'
+    version         = 'v0.2.10'
 }
 
 epi2melabs {

nextflow_schema.json

@@ -61,7 +61,7 @@
             "properties": {
                 "sample_sheet": {
                     "type": "string",
-                    "format": "path",
+                    "format": "file-path",
                     "description": "A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory containing sub-directories with FASTQ files.",
                     "help_text": "The sample sheet is a CSV file with, minimally, columns named `barcode` and `alias`. Extra columns are allowed. A `type` column is required for certain workflows and should have the following values; `test_sample`, `positive_control`, `negative_control`, `no_template_control`."
                 },
@@ -170,7 +170,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.2.9",
+            "default": "v0.2.10",
             "hidden": true
         },
         "monochrome_logs": {