Merge pull request #450 from nf-core/patch-nf-schema

CHANGELOG.md

@@ -30,6 +30,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #439](https://github.com/nf-core/viralrecon/pull/439)] - Fix cardinality issue when using `--bowtie2_index`
 - [[PR #435](https://github.com/nf-core/viralrecon/pull/435)] - Changed to a patched cutadapt from nf-core modules, added `skip_noninternal_primers` param to allow users to process primers inside the pipeline, and added `threeprime_adapters` to determine whether primers are 3' or 5' adapters.
 - [[PR #446](https://github.com/nf-core/viralrecon/pull/446)] - Update nextclade & pangolin modules
+- [[PR #450](https://github.com/nf-core/viralrecon/pull/450)] - Patch nf schema - include integer & string as type for sample
 
 ### Parameters
 
@@ -64,6 +65,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `multiqc`   | 1.14        | 1.19        |
 | `nextclade` | 2.12.0      | 3.8.2       |
 | `pangolin`  | 4.2         | 4.3         |
+| `nf-schema` |             | 2.2.1       |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

assets/schema_input.json

@@ -8,7 +8,7 @@
         "type": "object",
         "properties": {
             "sample": {
-                "type": "string",
+                "type": ["string", "integer"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]

conf/test_nanopore.config

@@ -35,7 +35,9 @@ params {
     primer_set_version = 3
 
     // variant calling options
-    freyja_repeats = 10
+    freyja_repeats    = 10
+    skip_freyja_boot  = true
+
 
     // Other parameters
     artic_minion_medaka_model = 's3://ngi-igenomes/test-data/viralrecon/minion_test/r941_min_high_g360_model.hdf5'

nextflow.config

@@ -313,7 +313,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {