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fix path #18

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Merged
kjdevv merged 1 commit into from
Nov 5, 2025
Merged

fix path #18

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2 changes: 1 addition & 1 deletion examples/apol1/apol1-classifier/project.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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5 changes: 2 additions & 3 deletions examples/apol1/apol1-classifier/workflow.nf
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Expand Up @@ -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}}"
"""
}

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5 changes: 2 additions & 3 deletions examples/brca/brca-classifier/workflow.nf
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Expand Up @@ -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}}"
"""
}

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2 changes: 1 addition & 1 deletion examples/herc2/herc2-classifier/project.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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5 changes: 2 additions & 3 deletions examples/herc2/herc2-classifier/workflow.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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}}"
"""
}

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4 changes: 2 additions & 2 deletions python/src/bioscript/biovault.py
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Expand Up @@ -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}}"
"""
}}

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