#!/bin/bash
#SBATCH --job-name=test_workflow
#SBATCH --partition=defq # the requested queue
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --tasks-per-node=1 #
#SBATCH --cpus-per-task=1 #
#SBATCH --mem-per-cpu=1000 # in megabytes, unless unit explicitly stated
#SBATCH --error=%J.err # redirect stderr to this file
#SBATCH --output=%J.out # redirect stdout to this file
......
and your workflow scripts
#!/bin/bash
sbatch -d singleton [slurm_script1]
sbatch -d singleton [slurm_script2]
Dependencies
If you have a series of bioinformatic processes you want to execute that for a ‘chain’ where each step is dependent on the output of the previous step this can be considered as a simple ‘workflow’. You can code these very simply in slurm labeling each job with the same name #SBATCH --job-name=[my_unique_jobname] and then calling each slurm scrip from a single file with teh command sbatch -d singleton [script_name]
Component scripts start:
Exercise: Make your instance based transcriptomic processes slurm compatible WORKFLOW
In Session 5 of you bioinformatics introductory lectures you were given scripts to pre-process, map, count and call duplicates - RNAseq Processing. I want you to transfer these and the data to scratch and convert these to slurm compatible scripts.
LEAVE OUT STAR LIBRARY FORMTTING STEP