Merge pull request #210 from alina-bauer/mhc-binding-subworkflow

New structure of mhc binding subworkflow

CHANGELOG.md

@@ -3,12 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.2.2dev - 2023-07-12
+## v2.2.2dev - 2023-08-29
 
 ### `Changed`
 
 - [203](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.9`
 - [203](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.8`
+- [#206](https://github.com/nf-core/epitopeprediction/issues/206) - Update the row checker class.
+- [#205](https://github.com/nf-core/epitopeprediction/issues/205) - Update general structure of MHC binding subworkflow
 
 ## v2.2.1 - WaldhaeuserOst Hotfix - 2023-03-16
 

bin/check_requested_models.py

@@ -6,6 +6,7 @@
 import csv
 import argparse
 import logging
+import urllib.request
 
 from epytope.Core.Allele import Allele
 from epytope.Core.Peptide import Peptide
@@ -74,7 +75,12 @@ def __main__():
         }
 
     # get the alleles
-    alleles = [Allele(a) for a in args.alleles.split(";")]
+    if args.alleles.startswith("http"):
+        alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").splitlines()]
+    elif args.alleles.endswith(".txt"):
+        alleles = [Allele(a) for a in open(args.alleles, "r").read().splitlines()]
+    else:
+        alleles = [Allele(a) for a in args.alleles.split(";")]
 
     peptide_lengths = []
     if args.peptides: