diff --git a/examples/apol1/apol1-classifier/project.yaml b/examples/apol1/apol1-classifier/project.yaml index df079c1..cc76ed7 100644 --- a/examples/apol1/apol1-classifier/project.yaml +++ b/examples/apol1/apol1-classifier/project.yaml @@ -2,7 +2,7 @@ name: apol1-classifier author: madhava@openmined.org workflow: workflow.nf template: dynamic-nextflow -version: 0.1.1 +version: 0.1.0 assets: - classify_apol1.py inputs: diff --git a/examples/apol1/apol1-classifier/workflow.nf b/examples/apol1/apol1-classifier/workflow.nf index 6753577..eb87533 100644 --- a/examples/apol1/apol1-classifier/workflow.nf +++ b/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 "${{participant_id}}" """ } diff --git a/examples/brca/brca-classifier/workflow.nf b/examples/brca/brca-classifier/workflow.nf index 3eeee26..64cd836 100644 --- a/examples/brca/brca-classifier/workflow.nf +++ b/examples/brca/brca-classifier/workflow.nf @@ -47,10 +47,9 @@ process brca_classifier { path "result_BRCA_${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 "${{participant_id}}" """ } diff --git a/examples/herc2/herc2-classifier/project.yaml b/examples/herc2/herc2-classifier/project.yaml index 444e3b4..78d7363 100644 --- a/examples/herc2/herc2-classifier/project.yaml +++ b/examples/herc2/herc2-classifier/project.yaml @@ -2,7 +2,7 @@ name: herc2-classifier author: madhava@openmined.org workflow: workflow.nf template: dynamic-nextflow -version: 0.1.1 +version: 0.1.0 assets: - classify_herc2.py inputs: diff --git a/examples/herc2/herc2-classifier/workflow.nf b/examples/herc2/herc2-classifier/workflow.nf index 3a531f3..e450e7c 100644 --- a/examples/herc2/herc2-classifier/workflow.nf +++ b/examples/herc2/herc2-classifier/workflow.nf @@ -47,10 +47,9 @@ process herc2_classifier { path "result_HERC2_${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 "${{participant_id}}" """ } diff --git a/python/src/bioscript/biovault.py b/python/src/bioscript/biovault.py index 3c8246b..52a2262 100644 --- a/python/src/bioscript/biovault.py +++ b/python/src/bioscript/biovault.py @@ -649,8 +649,8 @@ def aggregated = aggregate_results( script: def genoFileName = genotype_file.getName() """ - GENO_FILE=$(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}}" """ }}