Closed barrystokman closed 3 years ago
runs dir used in test: /home/proj/stage/flowcells/novaseq/runs/201203_A00689_0200_AHVKJCDRXX
demux dir used in test: /home/proj/stage/flowcells/novaseq/demux/201203_A00689_0200_AHVKJCDRXX
Demux started:
Demux dir and contents:
Project log: projectlog.20210122114617.log
cgstats select HVKJCDRXX
:
cgstats_HVKJCDRXX.txt
laneBarcode.html: laneBarcode.zip
cgstats and flowcell demultiplexing summary are identical to prod results: prod_files.zip
Since this will be release to SLURM the parent process will continue so any signal that this is finished will need to be put at the end of the sbatch script
it seems sbatch --wait
does the trick!
@barrystokman I am guessing you need to update and publish some AM docs together with PR. If so - let's include this in the PR header under implementation plan or similar
Bumped:
Deployed on hasta:
This PR adds demultiplexing of Novaseq flowcells on hasta
How to prepare for test:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-demux-stage.sh feat/demux-on-hasta
conda activate S_demux
pip install -U git+https://github.com/clinical-genomics/cgstats@feat/demux-on-hasta
us
How to test:
demuxstarted.txt
for a flowcellbash /home/proj/demux-stage/demultiplexing/scripts/novaseq/checkfornewrun.bash /home/proj/stage/flowcells/novaseq/runs/ /home/proj/stage/flowcells/novaseq/demux/ > /home/proj/demux-stage/log/logcheckfornewrun.novaseq.log
Expected test outcome:
demux
dir has been created for the flowcellReview:
This version is a:
Deployment plan:
hasta
:seq-nas-1
:clinical-nas-2
:nas-6
: