Merge pull request #16 from OpenMined/keelan/path-handling

update path handling

Author: kjdevv

examples/apol1/apol1-classifier/workflow.nf

@@ -47,8 +47,10 @@ process apol1_classifier {
         path "result_APOL1_${participant_id}.tsv"
 
     script:
+    def genoFileName = genotype_file.getName()
     """
-    bioscript classify "${assets_dir}/classify_apol1.py" --file "${genotype_file}" --participant_id "${participant_id}"
+    GENO_FILE=$(printf '%q' "${{genoFileName}}")
+    bioscript classify "${{assets_dir}}/classify_apol1.py" --file $GENO_FILE --participant_id "${{participant_id}}"
     """
 }
 

examples/brca/brca-classifier/workflow.nf

@@ -47,8 +47,10 @@ process brca_classifier {
         path "result_BRCA_${participant_id}.tsv"
 
     script:
+    def genoFileName = genotype_file.getName()
     """
-    bioscript classify "${assets_dir}/classify_brca.py" --file "${genotype_file}" --participant_id "${participant_id}"
+    GENO_FILE=$(printf '%q' "${{genoFileName}}")
+    bioscript classify "${{assets_dir}}/classify_brca.py" --file $GENO_FILE --participant_id "${{participant_id}}"
     """
 }
 

examples/herc2/herc2-classifier/workflow.nf

@@ -47,8 +47,10 @@ process herc2_classifier {
         path "result_HERC2_${participant_id}.tsv"
 
     script:
+    def genoFileName = genotype_file.getName()
     """
-    bioscript classify "${assets_dir}/classify_herc2.py" --file "${genotype_file}" --participant_id "${participant_id}"
+    GENO_FILE=$(printf '%q' "${{genoFileName}}")
+    bioscript classify "${{assets_dir}}/classify_herc2.py" --file $GENO_FILE --participant_id "${{participant_id}}"
     """
 }
 

python/src/bioscript/biovault.py

@@ -647,8 +647,10 @@ def aggregated = aggregate_results(
         path "result_{classifier_name}_${{participant_id}}.tsv"
 
     script:
+    def genoFileName = genotype_file.getName()
     """
-    bioscript classify "${{assets_dir}}/{workflow_script_asset}" --file "${{genotype_file}}" --participant_id "${{participant_id}}"
+    GENO_FILE=$(printf '%q' "${{genoFileName}}")
+    bioscript classify "${{assets_dir}}/{workflow_script_asset}" --file $GENO_FILE --participant_id "${{participant_id}}"
     """
 }}