fix novaseq demux script to enable automated post demux actions

barrystokman commented 3 years ago

The script https://github.com/Clinical-Genomics/deliver/blob/master/scripts/checkfornewdemuxonhasta.bash looks for both copycomplete.txt and demuxcomplete.txt to start post demux actions. For novaseq flowcells these actions are limited to adding the flowcell to HK (by running cg transfer flowcell <flowcell_id) and sending out an email indicating the the run is complete.

The file copycomplete.txt was previously added by the script https://github.com/Clinical-Genomics/demultiplexing/blob/98b5d9f5dff9d5bd932db98c32c3dbf422a73b11/scripts/2-hiseq-deliver.bash on thalamus that synced the demux directory on thalamus to the demultiplexed-runs directory on hasta.

This fix makes sure a copycomplete.txt is added to the run directory in demultiplexed-runs. It also remove any existing delivery.txt so the automation will pick it up for post demux actions

How to prepare for test:

[x] ssh to hasta
[x] install on stage: bash servers/resources/hasta.scilifelab.se/update-demux-stage.sh fix/novaseq-hasta-delivery-fix

How to test:

[x] remove one demuxstarted.txt: `rm /home/proj/stage/flowcells/novaseq/runs/201203_A00689_0200_AHVKJCDRXX/demuxstarted.txt
[x] run bash /home/proj/stage/bin/git/demultiplexing/scripts/novaseq/stage/checkfornewrun.bash /home/proj/stage/flowcells/novaseq/runs/ /home/proj/stage/demultiplexed-runs/

Expected test outcome:

[x] both demuxcomplete.txt and copycomplete.txt are created in /home/proj/stage/demultiplexed-runs/201203_A00689_0200_AHVKJCDRXX
[x] delivery.txt is removed if present in /home/proj/stage/demultiplexed-runs/201203_A00689_0200_AHVKJCDRXX
[x] 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:

[x] PATCH - when you make backwards compatible bug fixes or documentation/instructions

barrystokman commented 3 years ago

@karlnyr @henrikstranneheim I realized a quick fix was needed for post demux actions, if possible I'd like to deploy this today so it's ready to process the novaseq flowcell being sequenced today.

barrystokman commented 3 years ago

Bumped:

Deployed on hasta:

Clinical-Genomics / demultiplexing

fix novaseq demux script to enable automated post demux actions #137