Update eido/convert module (#2072)

* Update eido/validate module

* Update modules/eido/convert/meta.yml

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

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

modules/eido/convert/main.nf

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

modules/eido/convert/meta.yml

@@ -22,6 +22,9 @@ input:
   - format:
       type: value
       description: Extension of an output file
+  - 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/convert/main.nf

@@ -8,8 +8,9 @@ workflow test_eido_convert_nextflow_samplesheet {
 
     nextflow_samplesheet = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_nextflow_original_samplesheet.csv", checkIfExists: true)
     format = "csv"
+    pep_input_base_dir = []
 
-    EIDO_CONVERT ( nextflow_samplesheet, format )
+    EIDO_CONVERT ( nextflow_samplesheet, format, pep_input_base_dir )
 }
 
 
@@ -17,6 +18,7 @@ workflow test_eido_convert_pep_project {
 
     pep_project = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml", checkIfExists: true)
     format = "csv"
+    pep_input_base_dir = []
 
-    EIDO_CONVERT ( pep_project, format )
+    EIDO_CONVERT ( pep_project, format, pep_input_base_dir )
 }

tests/modules/eido/convert/test.yml

@@ -1,8 +1,8 @@
 - name: eido convert test_eido_convert_nextflow_samplesheet
   command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_nextflow_samplesheet -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
   tags:
-    - eido
     - eido/convert
+    - eido
   files:
     - path: output/eido/samplesheet_converted.csv
       md5sum: 7aa4da4944650b9c7c451c5dfbeae663
@@ -10,8 +10,8 @@
 - name: eido convert test_eido_convert_pep_project
   command: nextflow run ./tests/modules/eido/convert -entry test_eido_convert_pep_project -c ./tests/config/nextflow.config  -c ./tests/modules/eido/convert/nextflow.config
   tags:
-    - eido
     - eido/convert
+    - eido
   files:
     - path: output/eido/samplesheet_converted.csv
       md5sum: 2191ccc9c9c1ac4577726ea24cdb9fda