Clinical-Genomics / cg / 20135522384

86%

Build Type

push

github

Committed by web-flow

Commit Message

Fix flow cell retrieval handling incorrect sequencing run path (#4747)

## Description

This PR fixes the PDC fetching of flow cells archived in the `current` archiving directory. Two issues are fixed with this retrieval:
1. The `sequencing_run_output_dir` is built with the Illumina sequencing run full name instead of with the flow cell id
2. The `tar` command gets appended the `--strip-components=6` option to get rid of the internal directory nesting in the archived flow cell.

The behaviour for the flow cells archived in other locations is left untouched
---------

Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
Co-authored-by: islean <isak.ohlsson.angnell@gmail.com>

Run Details

12 of 15 new or added lines in 2 files covered. (80.0%)

1 existing line in 1 file now uncovered.

28353 of 33099 relevant lines covered (85.66%)

0.86 hits per line