broadinstitute / viral-core / 9650151278

70%

Build Type

push

github

Committed by web-flow

Commit Message

index bam before calling samtools idxstats; warn user if input lacks reads (#102)

* index bam before calling samtools idxstats; warn user if input lacks reads

in `read_utils.py::minimap2_idxstats()`, warn the user if the input bam file lacks reads, and index the post-alignment post-filtering bam before calling `samtools idxstats` so `minimap2_idxstats()` succeeds if the input bam lacks reads. The minimap2 wrapper, `tools/minimap2.py::Minimap2::align_bam()`, tolerates empty input and indexes bam/cram output, but the post-filtering final bam in minimap2_idxstats was not being indexed, which led to a problematic exit-on-failure condition in a WDL command invoking the function. Also fix import of the InvalidBamHeaderError class used in several tool modules (add it to errors.py, and import the error subclasses where needed).
This also runs minimap2 alignment when a read group lacks reads, since the newer version of minimap2 seems to better tolerate empty RGs. This allows samtools idxstats to yield zeros across the board for all input sequences when no reads are present, rather than only emitting the catchall "*" (which can cause issues downstream where metrics are expected)

* add pandas to deps

* attempt to fix coverage reporting due to breaking changes in coveralls reporter

see:
https://github.com/coverallsapp/coverage-reporter/issues/124
https://github.com/coverallsapp/github-action/issues/205
additional refs:
https://github.com/coverallsapp/github-action?tab=readme-ov-file
https://github.com/coverallsapp/coverage-reporter#supported-coverage-report-formats

Run Details

10 of 15 new or added lines in 4 files covered. (66.67%)

2 existing lines in 1 file now uncovered.

3061 of 4646 relevant lines covered (65.88%)

0.66 hits per line