Improved QC and inclusion of end of execution reports #15
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Using the fastq json file and some groovy, I've added an exclusion and reporting mechnism.
I've added two new QC options for miassembler:
--filter_ratio_threshold:
- The maximum allowed ratio of reads after filtering. If more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled. [default: 0.9]
--low_reads_count_threshold:
- The minimum number of reads required after filtering. If the read count falls below this threshold, the run is not assembled. [default: 1000]
If either threshold is exceeded the run is skipped, and the accessions are recorded in a CSV file (e.g., `SRR6180434,filter_ratio_threshold_exceeded`).
SandyRogers
requested changes
Aug 12, 2024
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Thank you @mberacochea !
My only request for now is to add an example head of the assembled_runs.csv and qc_failed_runs.csv files to the README.
Ge94
reviewed
Aug 12, 2024
Ge94
approved these changes
Aug 12, 2024
Co-authored-by: Sandy Rogers <[email protected]>
Co-authored-by: Germana Baldi <[email protected]>
KateSakharova
requested changes
Aug 19, 2024
…ports. The fetch tool unit tests are not failling ATM, ENA API issues.
SandyRogers
approved these changes
Aug 19, 2024
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Thanks @mberacochea ! One tiny wording suggestion on README.
Co-authored-by: Sandy Rogers <[email protected]>
mberacochea
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QC failed and assembed runs .csv "end of run" reports.
Using the fastq json file and some groovy, I've added an exclusion and reporting mechnism.
I've added two new QC options for miassembler:
--filter_ratio_threshold:
- The maximum allowed ratio of reads after filtering. If more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled. [default: 0.9]
--low_reads_count_threshold:
- The minimum number of reads required after filtering. If the read count falls below this threshold, the run is not assembled. [default: 1000]
If either threshold is exceeded the run is skipped, and the accessions are recorded in a CSV file (e.g.,
SRR6180434,filter_ratio_threshold_exceeded).[Warning]
The unit tests need to be adjusted, and these changes should be tested thoroughly. I have only tested this locally.