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Refactor based on comment from AA
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chuan-wang committed Nov 4, 2024
1 parent fe399db commit b3d8446
Showing 1 changed file with 4 additions and 13 deletions.
17 changes: 4 additions & 13 deletions taca/illumina/Runs.py
Original file line number Diff line number Diff line change
Expand Up @@ -704,18 +704,11 @@ def _process_simple_lane_with_single_demux(
os.symlink(source, dest)

# Replace the file laneBarcode.html
source_html_report_laneBarcode = os.path.join(
html_report_laneBarcode = os.path.join(

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source, "html", self.flowcell_id, "all", "all", "all", "laneBarcode.html"
)
dest_html_report_laneBarcode = os.path.join(
dest, "html", self.flowcell_id, "all", "all", "all", "laneBarcode.html"
)
if os.path.exists(source_html_report_laneBarcode) and os.path.exists(
dest_html_report_laneBarcode
):
html_report_laneBarcode_parser = LaneBarcodeParser(
source_html_report_laneBarcode
)
if os.path.exists(html_report_laneBarcode):
html_report_laneBarcode_parser = LaneBarcodeParser(html_report_laneBarcode)

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# Remove the trailing "_SX" postfix from samples names for BCL Convert when it handles SmartSeq3 libraries
for entry in html_report_laneBarcode_parser.sample_data:
if "_S" in entry["Sample"]:
Expand All @@ -724,9 +717,7 @@ def _process_simple_lane_with_single_demux(
html_report_laneBarcode_parser.sample_data,
key=lambda k: (k["Lane"].lower(), k["Sample"]),
)
_generate_lane_html(
dest_html_report_laneBarcode, html_report_laneBarcode_parser
)
_generate_lane_html(html_report_laneBarcode, html_report_laneBarcode_parser)

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def _fix_html_reports_for_complex_lanes(
self,
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