Merge pull request #18 from OpenMined/keelan/name-escape

fix path

Author: kjdevv

examples/apol1/apol1-classifier/project.yaml

@@ -2,7 +2,7 @@ name: apol1-classifier
 author: [email protected]
 workflow: workflow.nf
 template: dynamic-nextflow
-version: 0.1.1
+version: 0.1.0
 assets:
 - classify_apol1.py
 inputs:

examples/apol1/apol1-classifier/workflow.nf

@@ -47,10 +47,9 @@ process apol1_classifier {
         path "result_APOL1_${participant_id}.tsv"
 
     script:
-    def genoFileName = genotype_file.getName()
+    def filename = genotype_file.name
     """
-    GENO_FILE=$(printf '%q' "${{genoFileName}}")
-    bioscript classify "${{assets_dir}}/classify_apol1.py" --file $GENO_FILE --participant_id "${{participant_id}}"
+    bioscript classify "${{assets_dir}}/classify_apol1.py" --file "${filename}" --participant_id "${{participant_id}}"
     """
 }
 

examples/brca/brca-classifier/workflow.nf

@@ -47,10 +47,9 @@ process brca_classifier {
         path "result_BRCA_${participant_id}.tsv"
 
     script:
-    def genoFileName = genotype_file.getName()
+    def filename = genotype_file.name
     """
-    GENO_FILE=$(printf '%q' "${{genoFileName}}")
-    bioscript classify "${{assets_dir}}/classify_brca.py" --file $GENO_FILE --participant_id "${{participant_id}}"
+    bioscript classify "${{assets_dir}}/classify_brca.py" --file "${filename}" --participant_id "${{participant_id}}"
     """
 }
 

examples/herc2/herc2-classifier/project.yaml

@@ -2,7 +2,7 @@ name: herc2-classifier
 author: [email protected]
 workflow: workflow.nf
 template: dynamic-nextflow
-version: 0.1.1
+version: 0.1.0
 assets:
 - classify_herc2.py
 inputs:

examples/herc2/herc2-classifier/workflow.nf

@@ -47,10 +47,9 @@ process herc2_classifier {
         path "result_HERC2_${participant_id}.tsv"
 
     script:
-    def genoFileName = genotype_file.getName()
+    def filename = genotype_file.name
     """
-    GENO_FILE=$(printf '%q' "${{genoFileName}}")
-    bioscript classify "${{assets_dir}}/classify_herc2.py" --file $GENO_FILE --participant_id "${{participant_id}}"
+    bioscript classify "${{assets_dir}}/classify_herc2.py" --file "${filename}" --participant_id "${{participant_id}}"
     """
 }
 

python/src/bioscript/biovault.py

@@ -649,8 +649,8 @@ 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}}"
+    GENO_FILE=\$(printf '%q' "${{genoFileName}}")
+    bioscript classify "${{assets_dir}}/{workflow_script_asset}" --file \$GENO_FILE --participant_id "${{participant_id}}"
     """
 }}