Masking: show absolute paths of masked genome & index on completion

README.md

@@ -56,7 +56,7 @@ docker build . --platform linux/amd64
 ```bash
 git clone https://github.com/bede/hostile.git
 cd hostile
-conda env create -f environment.yml
+conda env create -y -f environment.yml
 conda activate hostile
 pip install --editable '.[dev]'
 pytest

src/hostile/lib.py

@@ -405,10 +405,10 @@ def mask(
         f"{n_masked_alignments} k-mers aligned after masking ({n_alignments} aligned before masking)"
     )
     logging.info(
-        f"Masked genome path (for use with long reads / Minimap2): {masked_ref_path}"
+        f"Masked genome path (for use with long reads / Minimap2): {masked_ref_path.resolve()}"
     )
     logging.info(
-        f"Masked Bowtie2 index path (for use with short reads): {masked_ref_index_path}"
+        f"Masked Bowtie2 index path (for use with short reads): {masked_ref_index_path.resolve()} (multiple files)"
     )
 
     return masked_ref_path, n_alignments, n_masked_alignments