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feat(store all fastq files for negative controls) #3681

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merged 3 commits into from
Sep 4, 2024
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feat(store all fastq files for negative controls) #3681

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3a7120e
Add check for negative controls when storing fastq files.
Sep 3, 2024
35cb735
Merge branch 'master' into 2871-store-fastq-hk-negative-controls
beatrizsavinhas Sep 4, 2024
558c708
Merge branch 'master' into 2871-store-fastq-hk-negative-controls
beatrizsavinhas Sep 4, 2024
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6 changes: 6 additions & 0 deletions cg/services/illumina/post_processing/housekeeper_storage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
get_undetermined_fastqs,
rename_fastq_file_if_needed,
)
from cg.store.models import Sample
from cg.store.store import Store
from cg.utils.files import get_files_matching_pattern

Expand All @@ -32,6 +33,11 @@ def _should_fastq_path_be_stored_in_housekeeper(
Check if a sample fastq file should be tracked in Housekeeper.
Only fastq files that pass the q30 threshold should be tracked.
"""
sample: Sample = store.get_sample_by_internal_id(internal_id=sample_id)

if sample.is_negative_control:
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return True

lane = get_lane_from_sample_fastq(sample_fastq_path)
q30_threshold: int = get_q30_threshold(sequencer_type)

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