Before the run

[x] email submission sheet to Hochwagen
[x] validate submission sheet Hochwagen
[x] if needed, remove previous run directories on pod:/hiseq to make space
[x] if needed, remove previous run directories on bowery:/scratch/gencore to make space
[x] remove previous runs on the hiseq machine
After the run
[x] Pod: Save runParameters.xml and InterOp in /hiseq/SAV_only/
[x] START tar the run on pod
[x] FINISH tar the run on pod
[x] START pull run tar file from pod to bowery
[x] FINISH pull run tar file from pod to bowery
[x] START untar run on bowery
[x] FINISH untar run on bowery
[x] move tar file to /data/cgsb/gencore-raw/
[x] validate submission sheet again and remove edit permissions
[x] import submission sheet and register the flowcell on hitscore
[x] START demultiplex with hitscore
[x] FINISH demultiplex with hitscore
[x] START calculate statistics with hitscore fastx
[x] FINISH calculate statistics with hitscore fastx
[x] review statistics
[x] deliver
[x] send emails

cgsb / hitscore