WIP: Input validation

README.md

@@ -19,6 +19,8 @@
 
 ## Introduction
 
+REMOVE THIS LINE
+
 **nf-core/gwas** is a bioinformatics pipeline that ...
 
 <!-- TODO nf-core:

assets/samplesheet.csv

@@ -1,3 +1,2 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+id,vcf,pheno,cov
+test,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/data/data_shrink_combined_4500/chr1_to_22_and_X.vcf.bgz,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/gwas/data/data_phenotypes_and_covariates/example1.pheno,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/gwas/data/data_phenotypes_and_covariates/example1.covar

assets/schema_input.json

@@ -7,27 +7,31 @@
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
+            "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "fastq_1": {
+            "vcf": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
-            "fastq_2": {
+            "pheno": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "cov": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["id", "vcf", "pheno"]
     }
 }

conf/modules.config

@@ -27,4 +27,11 @@ process {
         ]
     }
 
+    withName: 'PLINK_GWAS' {
+        ext.args   = '--allow-no-sex --linear'
+        publishDir = [
+            path: { "${params.outdir}/plink_gwas" },
+            mode: params.publish_dir_mode
+        ]
+    }
 }

modules.json

@@ -9,6 +9,16 @@
                         "branch": "master",
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
+                    },
+                    "plink/gwas": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    },
+                    "plink/vcf": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
                     }
                 }
             },