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1 parent 054274f commit 6663983Copy full SHA for 6663983
bolt/workflows/other/cancer_report.py
@@ -64,7 +64,7 @@ def entry(ctx, **kwargs):
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# Optional dragen hrd argument
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if kwargs['dragen_hrd_fp']:
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- hrdetect_line = f'--dragen_hrd {kwargs['dragen_hrd_fp']}'
+ hrdetect_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}"
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# Run gpgr canrep
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command = fr'''
@@ -100,7 +100,7 @@ def entry(ctx, **kwargs):
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--img_dir {output_image_dir}/ \
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--result_outdir {output_table_dir}/ \
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--out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html
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- {hrdetect_line}\
+ {hrdetect_arg}\
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'''
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util.execute_command(command)
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