change internal mhcclass to mhc_class for consistency

nf-core · Dec 5, 2023 · 1ffdacb · 1ffdacb
1 parent 3f3bcf9
commit 1ffdacb
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Showing 6 changed files with 12 additions and 13 deletions.
diff --git a/bin/check_requested_models.py b/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)

diff --git a/modules/local/epytope_check_requested_models.nf b/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} \

diff --git a/modules/local/epytope_generate_peptides.nf b/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} \\

diff --git a/modules/local/epytope_peptide_prediction.nf b/modules/local/epytope_peptide_prediction.nf
@@ -47,14 +47,14 @@ process EPYTOPE_PEPTIDE_PREDICTION {
     def class1_tools = tools_split.findAll { ! it.matches('.*(?i)(class-2|ii).*') }
     def class2_tools = tools_split.findAll { it.matches('.*(?i)(syf|class-2|ii).*') }
 
-    if (((meta.mhcclass == "I") & class1_tools.empty) | ((meta.mhcclass == "II") & class2_tools.empty)) {
-        exit 1, "No tools specified for mhc class ${meta.mhcclass}"
+    if (((meta.mhc_class == "I") & class1_tools.empty) | ((meta.mhc_class == "II") & class2_tools.empty)) {
+        exit 1, "No tools specified for mhc class ${meta.mhc_class}"
     }
 
-    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
 
-    def tools_to_use = ((meta.mhcclass == "I") | (meta.mhcclass == "H-2")) ? class1_tools.join(',') : class2_tools.join(',')
+    def tools_to_use = ((meta.mhc_class == "I") | (meta.mhc_class == "H-2")) ? class1_tools.join(',') : class2_tools.join(',')
 
     """
     # create folder for MHCflurry downloads to avoid permission problems when running pipeline with docker profile and mhcflurry selected

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -52,7 +52,6 @@
                 "genome_reference": {
                     "type": "string",
                     "default": "grch37",
-                    "enum": ["grch37", "grch38"],
                     "help_text": "This defines against which human Ensembl genome reference the pipeline performs the analysis including the incorporation of genetic variants e.g.. If `grch37` or `grch38` are specified the most recent Ensembl Biomart version for genome versions will be used. Alternatively, an Ensembl Biomart (archive) version can be specified, e.g. http://jan2020.archive.ensembl.org/.",
                     "description": "Specifies the Ensembl genome reference version that will be used."
                 },

diff --git a/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf
@@ -283,9 +283,9 @@ workflow EPITOPEPREDICTION {
         .variant
         .branch {
             meta_data, input_file ->
-                vcf : input_file.extension == 'vcf' || input_file.extension == 'vcf.gz'
+                vcf : input_file.endsWith('.vcf') || input_file.endsWith('.vcf.gz')
                     return [ meta_data, input_file ]
-                tab :  input_file.extension == 'tsv' || input_file.extension == 'GSvar'
+                tab :  input_file.endsWith('.tsv') || input_file.endsWith('.GSvar')
                     return [ meta_data, input_file ]
         }
         .set { ch_variants }