Here describes commonly-used examples as showcase.

BWA alignment

This recipe runs BWA alignment on AWS EC2 instances, without configuring instances.

hotsub run \
    --script ./main.sh \
    --image hotsub/bwa-alignment \
    --tasks ./bwa-alignment.csv \
    --aws-ec2-instance-type t2.large \
    --verbose

This command will

execute workflow described as main.sh
inside docker runtime of image hotsub/bwa-alignment
for each sample in bwa-alignment.csv
on EC2 instances with type t2.large

All the resources are automatically cleaned up after output files are located back to S3.

View this recipe on GitHub

STAR alignment

This recipe runs STAR RNA-seq alignment on AWS EC2 instances, without configuring instances.

hotsub run \
  --script ./main.sh \
  --image friend1ws/star-alignment \
  --tasks ./star-alignment.csv \
  --aws-ec2-instance-type m4.2xlarge \
  --disk-size 128 \
  --shared REFERENCE=s3://hotsub/resources/reference/GRCh37.STAR-2.5.2a \
  --verbose

This command will

execute workflow described as main.sh
inside docker runtime of image friend1ws/star-alignment
for each sample in star-alignment.csv
on EC2 instances with type m4.2xlarge
which have 128 GB disk size
and reference files are located on shared data instance to reduce inefficient network traffic and instance times

All the resources are automatically cleaned up after output files are located back to S3.

View this recipe on GitHub

GDC Download

This recipe downloads common data from NCI Genomic Data Commons and convert BAM files to Fastq files.

hotsub run \
  --script ./main.sh \
  --image hotsub/gdc-client \
  --tasks ./MCF7-fastq.csv \
  --aws-ec2-instance-type m4.2xlarge \
  --disk-size 64 \
  -v

This command will

execute workflow described as main.sh
inside docker runtime of image hotsub/gdc-client
for each sample in MCF7-fastq.csv
on EC2 instances with type m4.2xlarge
which have 64 GB disk size

All the resources are automatically cleaned up after output files are located back to S3.

View this recipe on GitHub

If you have any working hotsub recipe, please let us know and add it here ;)