Merge pull request #75 from Clinical-Genomics-Lund/symlink-dir-fixes

Symlink dir fixes

CHANGELOG.md

@@ -4,31 +4,35 @@
 
 ### Fixed
 
+ - Changed `--symlink_dir` to `--symlink-dir` for consistency
+
 ### Changed
 
+ - Use `basename` when `symlink_dir` provided
+
 ## [0.9.1]
 
 ### Added
 
-- Added additional tests to ensure that Bonsai input data can be re-cast into a `PipelineResult` data format.
+ - Added additional tests to ensure that Bonsai input data can be re-cast into a `PipelineResult` data format.
 
 ### Fixed
 
 ### Changed
 
-- Fixed some Pylint warnings.
-- Pylint ignores pysam functions since they are generated.
+ - Fixed some Pylint warnings.
+ - Pylint ignores pysam functions since they are generated.
 
 ## [0.9.0]
 
 ### Added
 
-- Added Shigapass output
-- Added tests for the Shigapass parser.
+ - Added Shigapass output
+ - Added tests for the Shigapass parser.
 
 ### Fixed
 
-- Fixed minor issues with the ShigaPass parser.
+ - Fixed minor issues with the ShigaPass parser.
 
 ### Changed
 
@@ -38,7 +42,7 @@
 
 ### Fixed
 
-- Reordered lineage data models in the method index.
+ - Reordered lineage data models in the method index.
 
 ### Changed
 
@@ -48,11 +52,11 @@
 
 ### Fixed
 
-- Updated lineage parser to work with TbProfiler v6.2
+ - Updated lineage parser to work with TbProfiler v6.2
 
 ### Changed
 
-- Changes lineage datamodel to reflect changes in TbProfiler output
+ - Changes lineage datamodel to reflect changes in TbProfiler output
 
 ## [0.8.1]
 

prp/cli.py

@@ -121,7 +121,7 @@ def cli():
 )
 @click.option("--snv-vcf", type=click.Path(), help="VCF with SNV variants")
 @click.option("--sv-vcf", type=click.Path(), help="VCF with SV variants")
-@click.option("--symlink_dir", type=click.Path(), help="Dir for symlink")
+@click.option("--symlink-dir", type=click.Path(), help="Dir for symlink")
 @click.option("--correct_alleles", is_flag=True, help="Correct alleles")
 @click.option(
     "-o", "--output", required=True, type=click.Path(), help="output filepath"
@@ -366,7 +366,7 @@ def create_bonsai_input(
 )
 @click.option(
     "-s",
-    "--symlink_dir",
+    "--symlink-dir",
     required=False,
     type=click.Path(exists=True, file_okay=False, dir_okay=True),
     help="Path to symlink directory",

prp/parse/utils.py

@@ -105,7 +105,7 @@ def get_db_version(db_version: dict) -> str:
 def _get_path(symlink_dir: str, subdir: str, filepath: str) -> str:
     """Get absolute/symlink path"""
     return (
-        os.path.join(symlink_dir, subdir, filepath)
+        os.path.join(symlink_dir, subdir, os.path.basename(filepath))
         if symlink_dir
         else os.path.realpath(filepath)
     )