Fix #146 (#5)

Mikado/configuration/daijin_configurator.py

@@ -232,10 +232,29 @@ def create_daijin_config(args, level="ERROR", piped=False):
 
     config["mikado"]["modes"] = args.modes
 
-    for method in args.asm_methods:
-        config["asm_methods"][method] = [""]
+    failed = False
+    if config["short_reads"]["r1"] and not args.aligners:
+        logger.critical(
+            "No short read aligner selected, but there are short read samples. Please select at least one alignment method.")
+        failed = True
+    if config["short_reads"]["r1"] and not args.asm_methods:
+        logger.critical(
+            "No short read assembler selected, but there are short read samples. Please select at least one assembly method.")
+        failed = True
+    if config["long_reads"]["files"] and not args.long_aln_methods:
+        logger.critical(
+            "No long read aligner selected, but there are long read samples. Please select at least one assembly method.")
+        failed = True
+
+    if failed:
+        sys.exit(1)
+
     for method in args.aligners:
         config["align_methods"][method] = [""]
+    for method in args.asm_methods:
+        config["asm_methods"][method] = [""]
+    for method in args.long_aln_methods:
+        config["long_read_align_methods"][method] = [""]
 
     # Set and eventually copy the scoring file.
     if args.scoring is not None:

Mikado/daijin/__init__.py

@@ -176,6 +176,9 @@ def create_config_parser():
         help="Strandedness of the reads. Specify it 0, 1, or number of samples times. Choices: %(choices)s.")
     parser.add_argument("-al", "--aligners", choices=["gsnap", "star", "hisat", "tophat"], required=False,
                         default=[], nargs="*", help="Aligner(s) to use for the analysis. Choices: %(choices)s")
+    parser.add_argument("-lal", "--long-read-aligners", dest="long_aln_methods", choices=["star", "gmap"],
+                        required=False, default=[], nargs="*",
+                        help="Aligner(s) to use for long reads. Choices: %(choices)s")
     parser.add_argument("-as", "--assemblers", dest="asm_methods", required=False,
                         choices=["class", "cufflinks", "stringtie", "trinity", "scallop"],
                         default=[], nargs="*", help="Assembler(s) to use for the analysis. Choices: %(choices)s")

Mikado/subprograms/configure.py

@@ -117,6 +117,7 @@ def create_config(args):
         namespace.samples = []
         namespace.strandedness = []
         namespace.asm_methods = []
+        namespace.long_aln_methods = []
         namespace.aligners = []
         if args.mode is not None:
             namespace.modes = args.mode[:]

Mikado/tests/test_system_calls.py

@@ -1054,6 +1054,7 @@ def test_daijin_config(self):
         namespace.threads = 1
         namespace.full = False
         namespace.seed = None
+        namespace.long_aln_methods = []
 
         for iteration in range(20):
             with self.subTest(iteration=iteration):