Feat/demux on hasta

[barrystokman]

This PR adds demultiplexing of Novaseq flowcells on hasta

How to prepare for test:

• [x] ssh to hasta
• [x] install on stage:
  1. bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-demux-stage.sh feat/demux-on-hasta
  2. conda activate S_demux
  3. pip install -U git+https://github.com/clinical-genomics/cgstats@feat/demux-on-hasta
  4. us

How to test:

• [x] login to hasta
• [x] remove demuxstarted.txt for a flowcell
• [x] run bash /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:

• [x] demultiplexing has started and finished without errors
• [x] a demux dir has been created for the flowcell
• [x] the demultiplexing statistics have been added to the cgstats database

Review:

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

This version is a:

• [x] MINOR - when you add functionality in a backwards compatible manner

Deployment plan:

• On hasta:
  • [x] https://github.com/Clinical-Genomics/demultiplexing/pull/134
  • [x] https://github.com/Clinical-Genomics/cgstats/pull/27
  • [x] https://github.com/Clinical-Genomics/servers/pull/476
• On seq-nas-1:
  • [ ] https://github.com/Clinical-Genomics/servers/pull/476
• On clinical-nas-2:
  • [ ] https://github.com/Clinical-Genomics/servers/pull/476
• On nas-6:
  • [ ] https://github.com/Clinical-Genomics/servers/pull/476
• [ ] Update documentation

[barrystokman]

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

[barrystokman]

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!

[henrikstranneheim]

@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

[barrystokman]

Bumped:

Deployed on hasta: