added nf-validation to check for most file existence

RobJY · May 7, 2024 · d441175 · d441175
1 parent 111414b
commit d441175
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/assets/schema_input_cycle.json b/assets/schema_input_cycle.json
@@ -22,17 +22,23 @@
             },
             "image_tiles": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
-                "errorMessage": "Need to provide a path to a directory containing image files"
+                "exists": true,
+                "errorMessage": "Need to provide a path to image file(s)"
             },
             "dfp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
             },
             "ffp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
             }
         },

diff --git a/assets/schema_input_sample.json b/assets/schema_input_sample.json
@@ -24,12 +24,16 @@
             },
             "dfp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
             },
             "ffp": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+$",
+                "exists": true,
                 "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
             }
         },

diff --git a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
@@ -264,7 +264,7 @@ def validateInputSamplesheetRow ( row, mode ) {
         if (row.size() >= 3 && row[2] != []) {
             def file_list = row[2].split(" ")
             file_list.each { curr_file ->
-                def curr_path = new File(row[1].toString() + "/" + curr_file)
+                def curr_path = file(row[1].toString() + "/" + curr_file)
                 if (!curr_path.exists()) {
                     error("Error: file in samplesheet not found: $curr_path")
                 }
@@ -317,7 +317,7 @@ def make_ashlar_input_sample( samplesheet_row ) {
         }
         cycle_images = samplesheet_row[index_sample_cycle_images].split(' ').collect{ "${tmp_path}${it}" }
         cycle_images.each{ file_path ->
-            def file_test = new File(file_path)
+            def file_test = file(file_path)
             if (!file_test.exists()) {
                 Nextflow.error("Error: ${file_path} does not exist!")
             }