fix schema_input

qbic-pipelines · Nov 19, 2024 · 132e190 · 132e190
1 parent 9fff54d
commit 132e190
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Showing 3 changed files with 18 additions and 31 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -17,14 +17,12 @@
             "normal_id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Provide name for normal sample for the maf file",
-                "dependentRequired": ["vcf_normal_id"]
+                "errorMessage": "Provide name for normal sample for the maf file"
             },
             "tumor_id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Provide name for tumor sample (if available) for the maf file",
-                "dependentRequired": ["vcf_tumor_id"]
+                "errorMessage": "Provide name for tumor sample (if available) for the maf file"
             },
             "vcf_normal_id": {
                 "type": "string",
@@ -40,17 +38,19 @@
                 "type": "string",
                 "pattern": "^\\S+\\.vcf\\.gz$",
                 "errorMessage": "Input vcf file must be gzipped and have extenstion '.vcf.gz'",
-                "exists": true,
                 "format": "file-path"
             },
             "index": {
                 "type": "string",
                 "pattern": "^\\S+\\.vcf\\.gz.tbi$",
                 "errorMessage": "Index file for vcf must have extension '.vcf.gz.tbi'",
-                "exists": true,
                 "format": "file-path"
             }
         },
-        "required": ["sample", "vcf"]
+        "uniqueItems": true,
+        "dependentRequired": {
+            "tumor_id": ["vcf_tumor_id"],
+            "vcf_tumor_id": ["tumor_id"]
+        }
     }
 }
diff --git a/main.nf b/main.nf
@@ -13,23 +13,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { VCFTOMAF  } from './workflows/vcftomaf'
+include { VCFTOMAF                } from './workflows/vcftomaf'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { VCFTOMAF  } from './workflows/vcftomaf'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
-
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -103,7 +91,6 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,

diff --git a/workflows/vcftomaf.nf → workflows/vcftomaf/main.nf b/workflows/vcftomaf.nf → workflows/vcftomaf/main.nf
@@ -7,17 +7,17 @@
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { BCFTOOLS_VIEW               } from '../modules/nf-core/bcftools/view/main'
-include { GUNZIP                      } from '../modules/nf-core/gunzip/main'
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { PICARD_LIFTOVERVCF          } from '../modules/nf-core/picard/liftovervcf/main'
-include { TABIX_TABIX                 } from '../modules/nf-core/tabix/tabix/main'
-include { UNTAR                       } from '../modules/nf-core/untar/main'
-include { VCF2MAF                     } from '../modules/nf-core/vcf2maf/main'
+include { BCFTOOLS_VIEW               } from '../../modules/nf-core/bcftools/view/main'
+include { GUNZIP                      } from '../../modules/nf-core/gunzip/main'
+include { MULTIQC                     } from '../../modules/nf-core/multiqc/main'
+include { PICARD_LIFTOVERVCF          } from '../../modules/nf-core/picard/liftovervcf/main'
+include { TABIX_TABIX                 } from '../../modules/nf-core/tabix/tabix/main'
+include { UNTAR                       } from '../../modules/nf-core/untar/main'
+include { VCF2MAF                     } from '../../modules/nf-core/vcf2maf/main'
 include { paramsSummaryMap            } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText      } from '../subworkflows/local/utils_nfcore_vcftomaf_pipeline'
+include { paramsSummaryMultiqc        } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML      } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText      } from '../../subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 
 
 /*