Fix shell compatibility: remove printf %q from all workflows

printf '%q' is a bash-specific feature but containers use /bin/sh.
The filename from Nextflow staging is already safe to use directly.

Fixed in:
- examples/apol1/apol1-classifier/workflow.nf
- examples/brca/brca-classifier/workflow.nf
- examples/thalassemia/thalassemia-classifier/workflow.nf
- python/src/bioscript/biovault.py (workflow generator template)

Author: madhavajay

examples/apol1/apol1-classifier/workflow.nf

@@ -53,8 +53,7 @@ process apol1_classifier {
     script:
     def genoFileName = genotype_file.getName()
     """
-    GENO_FILE=\$(printf '%q' "${genoFileName}")
-    bioscript classify "${assets_dir}/classify_apol1.py" --file \$GENO_FILE --participant_id "${participant_id}"
+    bioscript classify "${assets_dir}/classify_apol1.py" --file "${genoFileName}" --participant_id "${participant_id}"
     """
 }
 

examples/brca/brca-classifier/workflow.nf

@@ -53,8 +53,7 @@ process brca_classifier {
     script:
     def genoFileName = genotype_file.getName()
     """
-    GENO_FILE=\$(printf '%q' "${genoFileName}")
-    bioscript classify "${assets_dir}/classify_brca.py" --file \$GENO_FILE --participant_id "${participant_id}"
+    bioscript classify "${assets_dir}/classify_brca.py" --file "${genoFileName}" --participant_id "${participant_id}"
     """
 }
 

examples/thalassemia/thalassemia-classifier/workflow.nf

@@ -53,8 +53,7 @@ process thalassemia_classifier {
     script:
     def genoFileName = genotype_file.getName()
     """
-    GENO_FILE=\$(printf '%q' "${genoFileName}")
-    bioscript classify "${assets_dir}/classify_thalassemia.py" --file \$GENO_FILE --participant_id "${participant_id}"
+    bioscript classify "${assets_dir}/classify_thalassemia.py" --file "${genoFileName}" --participant_id "${participant_id}"
     """
 }
 

python/src/bioscript/biovault.py

@@ -828,8 +828,7 @@ def aggregated = aggregate_results(
     script:
     def genoFileName = genotype_file.getName()
     """
-    GENO_FILE=\\$(printf '%q' "${{genoFileName}}")
-    bioscript classify "${{assets_dir}}/{workflow_script_asset}" --file \\$GENO_FILE --participant_id "${{participant_id}}"
+    bioscript classify "${{assets_dir}}/{workflow_script_asset}" --file "${{genoFileName}}" --participant_id "${{participant_id}}"
     """
 }}