Closed barrystokman closed 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.
Bumped:
Deployed on hasta:
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:
bash servers/resources/hasta.scilifelab.se/update-demux-stage.sh fix/novaseq-hasta-delivery-fix
How to test:
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:
demuxcomplete.txt and copycomplete.txt
are created in/home/proj/stage/demultiplexed-runs/201203_A00689_0200_AHVKJCDRXX
delivery.txt
is removed if present in/home/proj/stage/demultiplexed-runs/201203_A00689_0200_AHVKJCDRXX
Review:
This version is a: