bash run_nextflow.sh nextflow.configA three step nextflow pipeline that aligns the fastqs to a reference genome and then sorts and generates an index for the aligned bam.
Make sure you configure your AWS CLI installation with appropriate access key id and secret access key. The following example shows sample values. Replace them with your own values.
$ aws configure
AWS Access Key ID [None]: AKIAIOSFODNN7EXAMPLE
AWS Secret Access Key [None]: *************************RfiCYEXAMPLEKEY
Default region name [None]: us-west-1
Default output format [None]: json