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Python package


Jetstream

Jetstream is a pipeline development framework written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers (Slurm).

Table of contents

Getting Started

Jetstream can be installed with Pip:

pip install git+https://github.com/tgen/jetstream.git@master

After installing with Pip, the command line utility can be launched with jetstream, and help can be accessed with the -h/--help options. If the command is not found, see the detailed installation help below. There are two ways to work with Jetstream: 1) via the command-line utility or 2) as a Python package. The majority of this guide will cover the command-line interface which is the most common use case.

$ jetstream -h

Build

The building blocks of a Jetstream pipeline are templates. Templates are scripts that describe the steps required for a pipeline. Some pipelines can be a single template file. Other pipelines will require several template and supporting data files.

Templates describe a set of reusable tasks that can be run for multiple sets of input data. You can think of templates like a declarative scripting language for building pipelines.

Here is an example template file:

- name: hello_world
  cmd: echo "{{ greeting }} world"

Complex pipelines can be designed with modular templates and organized into packages. Packaged pipelines can also include supporting data, documentation, etc. that can be referenced in the template files. See pipelines for details.

Run

Jetstream encourages project-oriented workflows. With this pattern, work is divided into separate directories (projects), and pipelines are executed on specific projects. Projects are directories where a pipeline run will execute and output files will be saved. Using projects makes it easier to organize logs and run metadata. It also allows for incremental changes in a pipeline to be applied without re-running the entire workflow.

Projects can be created with the init command:

$ jetstream init <path to project>

Now, templates can be run with the run command:

$ jetstream run example.jst -c greeting hola

Pipelines can be run by name with the pipelines command:

$ jetstream pipelines foo_pipe

Inspect

Jetstream can track data about pipeline runs in order to:

  • Resume runs that fail or need to be paused
  • Investigate problems that occur when running the pipeline
  • Gather run and task data for secondary analysis

The following commands can be used for inspecting Jetstream projects:

  • jetstream project for viewing project summary or details

  • jetstream tasks for viewing summary or details for specific tasks

  • jetstream pipelines can be used to inspect pipeline details

Learn More

Vignette

This section will walk through a typical use case that demonstrates the basics of creating and running a pipeline on projects. As a basic introduction, we'll create and run a pipeline that performs somatic variant calling on genome sequencing data. Jetstream template files are the building blocks for pipelines. They are simple text documents that containin a set of tasks to run. It may help to think of templates like scripts that Jetstream can interpret and execute.

  • To get started, copy the following code to a new file. We'll dive into the details later, for now, just save it to a new file called somatic_caller.jst
Click here to see the code 
# Simple template for calling somatic variants from fastqs for matched 
# tumor/normal pairs
{% set tumor_bam %}{{ tumor.name }}.bam{% endset %}
{% set normal_bam %}{{ normal.nam }}.bam{% endset %}
{% set tumor_rg %}@RG\\tID:{{ tumor.name }}\\tSM:{{ tumor.name }}{% endset %}
{% set normal_rg %}@RG\\tID:{{ normal.name }}\\tSM:{{ normal.name }}{% endset %}

- name: align_tumor
  cmd: |
     set -ue

     # Align fastqs with bwa, sort with samtools
     bwa mem \
       -t {{ threads }} \
       -R "{{ tumor_rg }}" \
       "{{ bwa_index }}" \
       "{{ tumor.r1fq }}" \
       "{{ tumor.r2fq }}" |\
       samtools sort \
         -O BAM \
         -@ {{ threads }} \
         - \
         -o "{{ tumor.name }}.bam"

      # Generate an index with samtools
      samtools index \
        -@ {{ threads }} \
        "{{ tumor.name }}.bam"


- name: align_normal
  cmd: |
     set -ue

     # Align fastqs with bwa, sort with samtools
     bwa mem \
       -t {{ threads }} \
       -R "{{ normal_rg }}" \
       "{{ bwa_index }}" \
       "{{ normal.r1fq }}" \
       "{{ normal.r2fq }}" |\
       samtools sort \
         -O BAM \
         -@ {{ threads }} \
         - \
         -o "{{ normal.name }}.bam"

      # Generate an index with samtools
      samtools index \
        -@ {{ threads }} \
        "{{ normal.name }}.bam"


- name: call_somatic_variants
  cmd: | 
    set -ue

    gatk Mutect2 \
      --reference "{{ reference_fasta }}" \
      --input "{{ tumor_bam }}" \
      --input "{{ normal_bam }}" \
      --tumor-sample "{{ tumor.name }}" \
      --normal-sample "{{ normal.name }}" \
      --output "{{ vcf_path }}"
  • In order to run the template, we'll need to provide values to fill in the variables. For this example, were going to add all of the input data to a single config file in YAML format. Save the code below to a new file called inputs.yaml.
Click here to see the code

TODO: These values should be filled in with ${JETSTREAM_TUTORIAL}/<filename>.. but first we need to create a tutorial dataset and upload to some public place

tumor:
    name: 
    r1fq:
    r2fq:
normal:
    name:
    r1fq:
    r2fq:
bwa_index:
reference_fasta:
  • Now that we have a template and an input config file we can run the pipeline. In order for Jetstream to save progress and run logs, we need to create a new project directory. When running pipelines inside of a jetstream project directory logs will be organized, and progress data will allow you to pause/restart/resume runs. Use the following command to initialize a new project:
jetstream init js_somatic_tutorial
  • Before running the pipeline, we'll verify that the template and config data are valid with the render feature. This option will fill in all of the variables in the template with data from our config file, and show us the final commands that will be executed when the pipeline runs. Use the following command to render the template (notice the -C is a capital c):
jetstream render somatic_caller.jst -C inputs.yaml
  • You should have received an error that there was no value provided for the variable threads. This was intentionally omitted from our config file to demonstrate some of the options for providing config data. Several values can be given with a config file using -C/--config-file options, or single config values can be given with the -c/--config options. Since we don't know what kind of computer you're using to run this pipeline, so we'll let you decide the number of threads to use. Here's how you would supply that value via the command line, replace 4 with the number of processor cores you would like to use:
jetstream render somatic_caller.jst -C inputs.yaml -c int:threads 4
  • Now the template should render successfully and be printed to the console. If everything looks good, we're ready to run. Use the following command to execute the pipeline.
jetstream run somatic_caller.jst -C inputs.yaml -c int:threads 4 --project js_somatic_tutorial

  • The runner will start executing commands in the order descibed by the task dependencies. If any tasks fail, you'll see messages in the logs, and the runner will exit with a non-zero status. If all tasks complete successfully the runner will exit with a zero.

  • Since we used a project, all outputs will be saved in that directory. After the runner completes, we can cd js_somatic_tutorial and see the results.

  • Inside the directory you should see the output data files, along with a jetstream index directory that contains data generated by the runner. There are several subcommands that can be used to inspect projects and get information about the tasks that were executed. Try the following commands:

# See details about the project and current status
jetstream project
# See a brief summary for all tasks 
jetstream tasks
# See detailed information for all tasks
jetstream tasks -v
  • Thank you for following along.

Installation

TGen users on Diamondback can load the latest version of Python with module load Python though it is recommended to check which modules are available via module avail Python and using a specific module.

This is a Python package and requires Python3 (>=3.7). Installation guides for Mac/Windows/Linux are available from the Hitchiker's Guide to Python After Python3 is installed, you can install Jetstream with Pip (next step).

Install with Pip

pip install git+https://github.com/tgen/jetstream.git@master

Troubleshooting: Command not found after install

Pip installs package scripts and executables automatically. In some cases you will need to update your PATH to include the directory where these scripts are stored.

  • MacOS:

    Changes should be added to ~/.bash_profile.

    Installed system-wide: the bin directory will be /usr/local/bin/

    Installed with --user: the bin directory will be ~/Library/Python/<pythonversion>/bin

  • Linux:

    Changes should be added to ~/.bashrc

    Installed system wide: the bin directory will be /usr/bin/

    Installed with --user: the bin directory will be ~/.local/bin/

See this post for more information.