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rannick committed Jan 31, 2025
1 parent 4952667 commit d2940a8
Showing 1 changed file with 5 additions and 6 deletions.
11 changes: 5 additions & 6 deletions cg/meta/workflow/nf_analysis.py
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import copy
import glob
import logging
import re
from datetime import datetime
Expand Down Expand Up @@ -623,14 +622,14 @@ def get_formatted_file_deliverable(
for deliverable_field, deliverable_value in file_template.items():
if deliverable_value is None:
continue
formatted_value = (
deliverable_value.replace("SAMPLEID", sample_id)
deliverables[deliverable_field] = (
deliverables[deliverable_field]
.replace("CASEID", case_id)
.replace("SAMPLEID", sample_id)
.replace("SAMPLENAME", sample_name)
.replace("PATHTOCASE", case_path)
)
expanded_files = glob.glob(formatted_value)
deliverables[deliverable_field] = expanded_files if expanded_files else formatted_value

LOG.info(deliverables[deliverable_field])
return FileDeliverable(**deliverables)

def get_deliverables_for_sample(
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