Merge pull request #13 from PennChopMicrobiomeProgram/codex/modernize-library-setup-with-pyproject.toml

Use pyproject.toml and update CLI flag

Author: Ulthran

pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seqBackup"
+description = "Set of rules to organize our fastq storage on the server."
+authors = [{name = "Ceylan Tanes", email = "ctanes@gmail.com"}]
+readme = "README.md"
+requires-python = ">=3.9"
+dynamic = ["version"]
+
+[project.urls]
+homepage = "https://github.com/PennChopMicrobiomeProgram"
+
+[project.scripts]
+backup_illumina = "seqBackupLib.backup:main"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["seqBackupLib"]
+
+[tool.setuptools.dynamic]
+version = {attr = "seqBackupLib.version.__version__"}

scripts/backup_illumina.py

@@ -121,11 +121,9 @@ def main(argv=None):
         help="The sample sheet associated with the run.",
     )
     parser.add_argument(
-        "--has-index",
-        required=False,
-        type=bool,
-        default=True,
-        help="Are index reads generated",
+        "--no-index",
+        action="store_true",
+        help="Skip index reads (I1/I2) during backup",
     )
     parser.add_argument(
         "--min-file-size",
@@ -140,7 +138,7 @@ def main(argv=None):
         args.forward_reads,
         args.destination_dir,
         args.sample_sheet,
-        args.has_index,
+        not args.no_index,
         args.min_file_size,
     )