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fix: fix excluding events from the report #332

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merged 4 commits into from
Oct 23, 2024
Merged

fix: fix excluding events from the report #332

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b92dbc9
fix: fix excluding events from the report
huzuner Oct 17, 2024
b530bb4
fix: restore else statement
huzuner Oct 18, 2024
e6518e3
chore
huzuner Oct 18, 2024
0b43367
fix: add report activation option to the simple test
huzuner Oct 21, 2024
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15 changes: 1 addition & 14 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -150,20 +150,7 @@ def get_final_output(wildcards):
expand(
"results/datavzrd-report/{batch}.{event}.{calling_type}.fdr-controlled",
batch=get_report_batches(calling_type),
event=get_calling_events(calling_type),
calling_type=calling_type,
)
)
else:
final_output.extend(
expand(
"results/final-calls/{group}.{event}.{calling_type}.fdr-controlled.bcf",
group=(
variants_groups
if calling_type == "variants"
else fusions_groups
),
event=get_calling_events(calling_type),
event=event,
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⚠️ Potential issue

Potential Issue with Event Parameter Usage in 'expand' Function

In the get_final_output function, the event parameter in the expand call has been changed to use the variable event directly. Ensure that event is correctly defined in this context and that it provides the expected values. Previously, a function call like get_calling_events(calling_type) might have provided a list of events, whereas event here may be a single value from the loop. This could affect the expanded outputs if not handled properly.

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If we remove the use of this utility function here, maybe we can instead use it above, to replace this:

for event in config["calling"]["fdr-control"]["events"]:

with the function call like this:

for event in get_calling_events(calling_type):

This ensures, that the calling_type variable from the respective for-loop is also respected, fixing a potential bug.

calling_type=calling_type,
)
)
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