Merge pull request #220 from jonasscheid/fix_lost_vcfgz_support

Switch to nf-validation

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#220](https://github.com/nf-core/epitopeprediction/pull/220) - Switch to nf-validation to parse samplesheet
 - [#213](https://github.com/nf-core/epitopeprediction/pull/203) - Rename param `genome_version` to `genome_reference`, add functionality to handle BioMart archive urls
 - [#213](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.10`
 - [#203](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.9`

assets/schema_input.json

@@ -20,20 +20,32 @@
                     },
                     {
                         "type": "string",
-                        "pattern": "(^[A-Z][*][0-9][0-9][:][0-9][0-9])$"
+                        "pattern": "^([A-E]{1}[*][0-9]{2}[:][0-9]{2})(;[A-E]{1}[*][0-9]{2}[:][0-9]{2})*$"
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^((DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2})(;(DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2})*$"
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^((DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2}[-](DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2})(;((DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2}[-](DR|DP|DQ)[AB][0-9][*][0-9]{2}[:][0-9]{2}))*$"
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^[H][-][2][-][A-Za-z]{2,3}$"
                     }
                 ],
-                "errorMessage": "Alleles must be provided as string or file with extension '.txt''"
+                "errorMessage": "Alleles must be provided as string or file with extension '.txt'. Please check the documentation for more information."
             },
             "mhc_class": {
                 "type": "string",
                 "pattern": "^(I|II|H-2)$",
-                "errorMessage": "The MHC class must be provided. Valid values: "
+                "errorMessage": "The MHC class must be provided. Valid values: 'I', 'II' or 'H-2'"
             },
             "filename": {
                 "type": "string",
-                "pattern": "^\\S+\\.(vcf|tsv|fasta|fa|txt)$",
-                "errorMessage": "Variants/proteins/peptides for sample must be provided and have one of the following extensions:  '.vcf', '.tsv', '.fasta', '.fa', '.txt'"
+                "pattern": "^\\S+\\.(vcf|vcf.gz|tsv|fasta|fa)$",
+                "errorMessage": "Variants/proteins/peptides for sample must be provided and have one of the following extensions: '.vcf', '.vcf.gz', '.tsv', '.fasta', '.fa'"
             }
         },
         "required": ["sample", "alleles", "mhc_class", "filename"]

bin/check_requested_models.py

@@ -54,7 +54,7 @@ def __main__():
         "Write out information about supported models by epytope for installed predictor tool versions."
     )
     parser.add_argument("-p", "--peptides", help="File with one peptide per line")
-    parser.add_argument("-c", "--mhcclass", default=1, help="MHC class I or II")
+    parser.add_argument("-c", "--mhc_class", default=1, help="MHC class I or II")
     parser.add_argument("-l", "--max_length", help="Maximum peptide length", type=int)
     parser.add_argument("-ml", "--min_length", help="Minimum peptide length", type=int)
     parser.add_argument("-a", "--alleles", help="<Required> MHC Alleles", required=True, type=str)

conf/modules.config

@@ -20,14 +20,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

modules/local/epytope_check_requested_models.nf

@@ -30,8 +30,8 @@ process EPYTOPE_CHECK_REQUESTED_MODELS {
     }
 
     def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}_peptides"
-    def min_length = ("${meta.mhcclass}" == "I") ? params.min_peptide_length : params.min_peptide_length_class2
-    def max_length = ("${meta.mhcclass}" == "I") ? params.max_peptide_length : params.max_peptide_length_class2
+    def min_length = ("${meta.mhc_class}" == "I") ? params.min_peptide_length : params.min_peptide_length_class2
+    def max_length = ("${meta.mhc_class}" == "I") ? params.max_peptide_length : params.max_peptide_length_class2
 
     """
     check_requested_models.py ${argument} \

modules/local/epytope_generate_peptides.nf

@@ -19,8 +19,8 @@ process EPYTOPE_GENERATE_PEPTIDES {
 
     script:
     def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}_peptides"
-    def min_length = (meta.mhcclass == "I") ? params.min_peptide_length : params.min_peptide_length_class2
-    def max_length = (meta.mhcclass == "I") ? params.max_peptide_length : params.max_peptide_length_class2
+    def min_length = (meta.mhc_class == "I") ? params.min_peptide_length : params.min_peptide_length_class2
+    def max_length = (meta.mhc_class == "I") ? params.max_peptide_length : params.max_peptide_length_class2
 
     """
     gen_peptides.py --input ${raw} \\