Integrate nf-validation plugin

nf-core · Sep 14, 2023 · 5408656 · 5408656
1 parent 744a8eb
commit 5408656
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Showing 14 changed files with 63 additions and 737 deletions.
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
 id,fasta,reference,structures
-seatoxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref,
+seatoxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref,test-dataset/structures/setoxin-ref/
 toxin-ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/toxin-ref.fa,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/toxin.ref,
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,6 +10,7 @@
             "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
+                "meta": ["id"],
                 "errorMessage": "id/sample name must be provided and cannot contain spaces"
             },
             "fasta": {

diff --git a/assets/schema_tools.json b/assets/schema_tools.json
@@ -9,17 +9,21 @@
         "properties": {
             "tree": {
                 "type": "string",
-                "errorMessage": "tree name cannot contain spaces"
+                "errorMessage": "tree name cannot contain spaces",
+                "meta": ["tree"]
             },
             "args_tree": {
-                "type": "string"
+                "type": "string",
+                "meta": ["args_tree"]
             },
             "align": {
                 "type": "string",
+                "meta": ["align"],
                 "errorMessage": "align name must be provided and cannot contain spaces"
             },
             "args_align": {
-                "type": "string"
+                "type": "string",
+                "meta": ["args_align"]
             }
         },
         "required": ["align"]

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py