Sample Processing Flowcell 25.03.2020

[deyazoubi]

a list of open and closed To-Dos:

1. 200325_NB552271_0006_AHHJLFBGXC

• Transfer raw data to HPC
• check NAS space capacity
• backup
• create samplesheet and push to github
• inform wetlab to delete data on instrument
• inform analysts about demux quality
• delete data from pipeline server
• upload to Snupy
• inform analysts about data upload to Snupy and send status_update

Branch name SS_006

[deyazoubi]

capture_kit: we are using two default capture kits for human and for mouse. This might change in the future and thus you can define a project specific capture_kit.

In this flowcell new captuer kit is used "V7"
there are three ways to define the capture kit for a sample:

1. by adding a column "capture_kit" to the input samplesheet and set the cell value to a capture kit name defined in config.yaml this is what is set in for this flowcell**
   

   spike/config.yaml

   Line 373 in 2ac88ea

   SureSelect Human All Exon V7:

see 180222_K00171_0649_HT332BBXX_spike.csv
2. by specifing a key "capture_kit" at the project in config.yaml. Value must match one of the defined capture kits in config.yaml
3. by specifing the species for the sample project, which than select the default kit defined in config.yaml for the species.
see 180920_SN737_0447_ACC9UWACXX_spike

1,2,3 are listed in order of their precedence, i.e. of 1 and 3 is defined, 1 wins.