nf-core · christopher-mohr · Aug 25, 2020 · Mar 19, 2020 · Apr 1, 2020 · Apr 30, 2020
@@ -32,6 +32,9 @@ jobs:
       - name: Run peptides test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_peptides,docker
+      - name: Run peptides test on H2 allele
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_peptides_h2,docker
       - name: Run proteins test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_proteins,docker
@@ -808,7 +808,7 @@ def make_predictions_from_variants(variants_all, methods, alleles, minlength, ma
         df.reset_index(inplace=True)
 
         for c in df.columns:
-            if '*' in str(c):
+            if ('HLA-' in str(c)) or ('H-2-' in str(c)):
                 idx = df.columns.get_loc(c)
                 df.insert(idx + 1, '%s affinity' % c, df.apply(lambda x: create_affinity_values(str(c), int(x['length']), float(x[c]), x['Method'], max_values_matrices, allele_string_map), axis=1))
                 df.insert(idx + 2, '%s binder' % c, df.apply(lambda x: create_binder_values(float(x['%s affinity' % c]), x['Method']), axis=1))
@@ -890,7 +890,7 @@ def make_predictions_from_peptides(peptides, methods, alleles, protein_db, ident
             df[c] = df.apply(lambda row: row[0].get_metadata(c)[0], axis=1)
 
         for c in df.columns:
-            if '*' in str(c):
+            if ('HLA-' in str(c)) or ('H-2-' in str(c)):
                 idx = df.columns.get_loc(c)
                 df.insert(idx + 1, '%s affinity' % c, df.apply(lambda x: create_affinity_values(str(c), int(x['length']), float(x[c]), x['Method'], max_values_matrices, allele_string_map), axis=1))
                 df.insert(idx + 2, '%s binder' % c, df.apply(lambda x: create_binder_values(float(x['%s affinity' % c]), x['Method']), axis=1))

@@ -0,0 +1,18 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/epitopeprediction -profile test_peptides_h2
+ */
+
+params {
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  peptides = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides.tsv'
+  alleles = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.H2.txt'
+}
@@ -109,6 +109,14 @@ else {
     allele_file = file(params.alleles)
 }
 
+if ( params.input ){
+    allele_file.eachLine{line ->
+        if (line.contains("H2-")) {
+            exit 1, "Mouse allele provided: $line. Not compatible with reference ${params.genome}. Currently mouse alleles are only supported when using peptide sequences as input (--peptides)."
+        }
+    }
+}
+
 if ( params.mhc_class != 1 && params.mhc_class != 2 ){
     exit 1, "Invalid MHC class option: ${params.mhc_class}. Valid options: 1, 2"
 }

@@ -84,6 +84,7 @@ profiles {
   test { includeConfig 'conf/test.config' }
   test_variant_tsv { includeConfig 'conf/test_variant_tsv.config' }
   test_peptides { includeConfig 'conf/test_peptides.config' }
+  test_peptides_h2 { includeConfig 'conf/test_peptides_h2.config' }
   test_proteins { includeConfig 'conf/test_proteins.config' }
 }