Add raw read counts to alignment QC report - #260
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Trimmomatic now writes a per-sample -summary file. A new scraper function parses 'Input Read Pairs' from it and stores raw_reads (pairs * 2) on the sample, migrated in via a new alembic revision. The alignment report now shows both the raw read count and the post-filtering read count, clarifying the pass/fail discrepancy between raw sequencing depth and filtered QC metrics. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
(**) and (***) rendered with a distorted, italic-looking middle character in the browser due to consecutive asterisk glyphs. Use the standard *, dagger, double-dagger footnote sequence instead. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
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Description
Currently the alignment summary page only shows the read count after Trimmomatic filtering ("Antal Reads"). This creates a discrepancy: a sample is deemed passable if the raw reads fed into the workflow are sufficient and no other QC metric is red, but the report never surfaces that raw read count, so the reasoning behind a pass/fail isn't visible to reviewers.
This PR adds the raw (pre-filtering) read count alongside the existing filtered count:
-summary <trimdir>/{sample}_trim_summary.txtper sample.Scraper.scrape_trimmomatic()parsesInput Read Pairsfrom that summary and storesraw_reads(pairs * 2) on the sample.raw_readsis a newsamplescolumn, added via a new (idempotent) Alembic migration so it applies cleanly to both fresh and existing databases.Primary function of PR
Testing
bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAMEusconda activate S_microSALTmicroSALT analyse --input /path/to/fastq/ SAMPLEINFO_FILETest results
Full local test suite passes (90/90), including new unit tests for the Trimmomatic summary parsing and a manual verification of the Alembic migration against both a fresh SQLite database and one pre-seeded at the prior revision (idempotent, no duplicate-column errors).
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