Update eido/validate module (#2071)

* Update eido/validate module

* Update modules/eido/validate/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/eido/validate/main.nf

@@ -10,6 +10,7 @@ process EIDO_VALIDATE {
     input:
     path samplesheet
     path schema
+    path pep_input_base_dir
 
     output:
     path "versions.yml"  , emit: versions

modules/eido/validate/meta.yml

@@ -23,6 +23,9 @@ input:
       type: file
       description: Schema that the samplesheet will be validated against
       pattern: "*.{yaml,yml}"
+  - pep_input_base_dir:
+      type: file
+      description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
 
 output:
   - versions:

tests/modules/eido/validate/main.nf

@@ -8,14 +8,16 @@ workflow test_eido_validate_on_nextflow_samplesheet {
 
     samplesheet = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
     schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+    pep_input_base_dir = []
 
-    EIDO_VALIDATE ( samplesheet, schema )
+    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
 }
 
 workflow test_eido_validate_on_pep_config {
 
     samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
     schema = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/pep/test_samplesheet_schema.yaml", checkIfExists: true)
+    pep_input_base_dir = []
 
-    EIDO_VALIDATE ( samplesheet, schema )
+    EIDO_VALIDATE ( samplesheet, schema, pep_input_base_dir )
 }