Author: Alan Tracey - GRIT - Sanger
Contributors: @DLBPointon - Nextflow DSL2 and JIRA integration
Written to run on Sangers farm5/tol-farm
Activte the curation_v2 environment, this contains the path locations of various python modules and software required for the pipeline.
You will need to edit the sample.env to include your personal JIRA credentials and then save it as .env and then use chmod 700 .env to lock out anyone else from viewing said credentials.
This requires the use of a GRIT specific instalation of nextflow.
The below will run the small_test profile which runs default data.
bsub -e error -o out -n 16 -q small -M1500 -R'select[mem>1500] rusage[mem=1500] span[hosts=1]' '/software/grit/bin/nextflow_grit run main.nf -entry top_tail -c nextflow.conf -profile small_test'
Results will populate the Telomere motif and Telomere motif k-mer length fields in JIRA.
Upper case will denote Cannonical.Upper case should be used where possible.
Lower case will denote non-cannonical.
