passing enviroment variable - Githubissues

Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

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passing enviroment variable #168

Closed gustavlagneborg closed 1 year ago

gustavlagneborg commented 1 year ago

This PR fixes so that correct enviroment variable is used when creating the sbatch job for hiseqx flowcells. In addition, it fixes the unbound variable that hindered demuxes to start

How to prepare for test:

[ ] ssh to hasta
[ ] install on stage: bash servers/resources/hasta.scilifelab.se/update-demux-stage.sh [THIS-BRANCH-NAME]

How to test:

[ ] login to ...
[ ] do ...

Expected test outcome:

[ ] check that ...
[ ] Take a screenshot and attach or copy/paste the output.

Review:

[ ] code approved by
[ ] tests executed by
[ ] "Merge and deploy" approved by Thanks for filling in who performed the code review and the test!

This version is a:

[ ] MAJOR - when you make incompatible API changes
[x] MINOR - when you add functionality in a backwards compatible manner
[ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

gustavlagneborg commented 1 year ago

Demultiplexing works:

Screenshot 2023-01-11 at 12 39 38