Workflow Syntax and Execution Runtime

This section introduces the YAML syntax used by Popper, describes the workflow execution runtime and shows how to execute workflows in alternative container engines.


A Popper workflow file looks like the following:

- uses: docker://alpine:3.9
  args: ["ls", "-la"]

- uses: docker://alpine:3.11
  args: ["echo", "second step"]

    FOO: BAR

A workflow specification contains one or more steps in the form of a YAML list named steps. Each item in the list is a dictionary containing at least a uses attribute, which determines the docker image being used for that step. An options dictionary specifies options that are applied to the workflow.

Workflow steps

The following table describes the attributes that can be used for a step. All attributes are optional with the exception of the uses attribute.

Attribute Description
uses required The Docker image that will be executed for that step. For example,
uses: docker://node:10. See "Referencing images in a step" section below for
more examples.
id optional Assigns an identifier to the step. By default, steps are asigned a numerid id
corresponding to the order of the step in the list, with 1 identifying
the first step.
runs optional Specifies the command to run in the docker image. If runs is omitted, the
command specified in the Dockerfile's ENTRYPOINT instruction will execute.
Use the runs attribute when the Dockerfile does not specify an ENTRYPOINT
or you want to override the ENTRYPOINT command. The runs attribute does not
invoke a shell by default. Using runs: "echo $VAR" will not print the value
stored in $VAR, but will instead print \"\$VAR.\". To use environment
variables with the runs instruction, you must include a shell to expand
the variables, for example: runs: ["sh", "-c", "echo $VAR"]. If the value of runs
refers to a local script, the path is relative to the workspace folder (see
The Workspace section below)
args optional The arguments to pass to the command. This is an array of strings. For example,
args: ["--flag", "--arg", "value"]. If the value of args
refers to a local script, the path is relative to the workspace folder (see
The Workspace section below). Similarly to the runs attribute, if an envrionment variable is being
referenced, in order for this reference to be valid, a shell must be invoked (in the runs attribute)
in order to expand the value of the variable.
env optional The environment variables to set inside the container's runtime environment. If
you need to pass environment variables into a step, make sure it runs a command
shell to perform variable substitution. For example, if your runs attribute is
set to ["sh", "-c"], the value of args will be passed to sh -c and
executed in a command shell. Alternatively, if your Dockerfile uses an
ENTRYPOINT to run the same command ("sh -c"), args will execute in a
command shell as well. See ENTRYPOINT for more details.
secrets optional Specifies the names of the secret variables to set in the runtime environment
which the container can access as an environment variable. For example,
secrets: ["SECRET1", "SECRET2"].
skip_pull optional Assume that the given container image already exist and skip pulling it.
dir optional Specifies the working directory for a step. By default, the directory is always /workspace if another one is not defined.

Referencing images in a step

A step in a workflow can reference a container image defined in a Dockerfile that is part of the same repository where the workflow file resides. In addition, it can also reference a Dockerfile contained in public Git repository. A third option is to directly reference an image published a in a container registry such as DockerHub. Here are some examples of how you can refer to an image on a public Git repository or Docker container registry:

Template Description
./path/to/dir The path to the directory that contains the Dockerfile. This is a relative
path with respect to the workspace directory (see
The Workspace section below). Example: ./path/to/myimg/.
{url}/{user}/{repo}@{ref} A specific branch, ref, or SHA in a public Git repository. If url
is ommited, is used by default.
{url}/{user}/{repo}/{path}@{ref} A subdirectory in a public Git repository at a specific branch, ref,
or SHA.
docker://{image}:{tag} A Docker image published on Docker Hub.
Example: docker://alpine:3.8.
docker://{host}/{image}:{tag} A Docker image in a public registry other than DockerHub. Note
that the container engine needs to have properly configured to
access the referenced registry in order to download from it.
Example: docker://

It’s strongly recommended to include the version of the image you are using by specifying a SHA or Docker tag. If you don’t specify a version and the image owner publishes an update, it may break your workflows or have unexpected behavior.

In general, any Docker image can be used in a Popper workflow, but keep in mind the following:

  • When the runs attribute for a step is used, the ENTRYPOINT of the image is overridden.
  • The WORKDIR is overridden and /workspace is used instead (see The Workspace section below).
  • The ARG instruction is not supported, thus building an image from a Dockerfile (public or local) only uses its default value.
  • While it is possible to run containers that specify USER other than root, doing so might cause unexpected behavior.

Referencing private Github repositories

You can reference Dockerfiles located in private Github repositories by defining a GITHUB_API_TOKEN environment variable that the popper run command reads and uses to clone private repositories. The repository referenced in the uses attribute is assumed to be private and, to access it, an API token from Github is needed (see instructions here). The token needs to have permissions to read the private repository in question. To run a workflow that references private repositories:

export GITHUB_API_TOKEN=access_token_here
popper run -f wf.yml

If the access token doesn’t have permissions to access private repositories, the popper run command will fail.

Workflow options

The options attribute can be used to specify env and secrets that are available to all the steps in the workflow. For example:

    FOO: var1
    BAR: var2
  secrets: [SECRET1, SECRET2]

- uses: docker://alpine:3.11
  runs: sh
  args: ["-c", "echo $FOO $SECRET1"]

- uses: docker://alpine:3.11
  runs: sh
  args: ["-c", "echo $ONLY_FOR"]
    ONLY_FOR: this step

The above shows environment variables that are available to all steps that get defined in the options dictionary; it also shows an example of a variable that is available only to a single step (second step). This attribute is optional.

Execution Runtime

This section describes the runtime environment where a workflow executes.

The Workspace

When a step is executed, a folder in your machine is bind-mounted (shared) to the /workspace folder inside the associated container. By default, the folder being bind-mounted is $PWD, that is, the working directory from where popper run is being invoked from. If the -w (or --workspace) flag is given, then the value for this flag is used instead. See the official Docker documentation for more information about how volumes work with containers.

The following diagram illustrates this relationship between the filesystem namespace of the host (the machine where popper run is executing) and the filesystem namespace within container:

                                |  /bin                |
                                |  /etc                |
                                |  /lib                |
 Host                           |  /root               |
+-------------------+   bind    |  /sys                |
|                   |   mount   |  /tmp                |
| /home/me/my/proj <------+     |  /usr                |
| ├─ wf.yml         |     |     |  /var                |
| └─      |     +------> /workspace          |
|                   |           |  ├── wf.yml          |
|                   |           |  └──       |
+-------------------+           +----------------------+

For example, let’s look at a workflow that creates files in the workspace:

- uses: docker://alpine:3.12
  args: [touch, ./myfile]

The above workflow has only one single step that creates the myfile file in the workspace directory if it doesn’t exist, or updates its metadata if it already exists, using the touch command. Assuming the above workflow is stored in a wf.yml file in /home/me/my/proj/, we can run it by first changing the current working directory to this folder:

cd /home/me/my/proj/
popper run -f wf.yml

And this will result in having a new file in /home/me/my/proj/myfile. However, if we invoke the workflow from a different folder, the folder being bind-mounted inside the container is a different one. For example:

cd /home/me/
popper run -f /home/me/my/proj/wf.yml

In the above, the file will be written to /home/me/myfile, because we are invoking the command from /home/me/, and this path is treated as the workspace folder. If we provide a value for the --workspace flag (or its short version -w), the workspace path then changes and thus the file is written to this given location. For example:

cd /
popper run -f /home/me/my/proj/wf.yml -w /home/me/my/proj/

The above writes the /home/me/my/proj/myfile even though Popper is being invoked from /. Note that the above is equivalent to the first example of this subsection, where we first changed the directory to /home/me/my/proj and ran popper run -f wf.yml.

Changing the working directory

To specify a working directory for a step, you can use the dir attribute in the workflow. This changes where the specified command is executed. For example, adding dir as follows:

- uses: docker://alpine:3.9
  args: [touch, ./myfile]
  dir: /tmp/

And assuming that it is stored in /home/me/my/proj/wf.yml, invoking the workflow as:

cd /home/me
popper run -f wf.yml -w /home/me/my/proj

Would result in writing myfile in the /tmp folder that is inside the container filesystem namespace, as opposed to writing it to /home/me/my/projc/ (the value given for the --workspace flag). As it is evident in this example, if the directory specified in the dir attribute resides outside the /workspace folder, then anything that gets written to it won’t persist after the step ends its execution (see “Filesystem namespaces and persistence” below for more).

For completeness, we show an example of using dir to specify a folder within the workspace:

- uses: docker://alpine:3.9
  args: [touch, ./myfile]
  dir: /workspace/my/proj/

And executing:

cd /home/me
popper run -f wf.yml

would result in having a file in /home/me/my/proj/myfile.

Filesystem namespaces and persistence

As mentioned previously, for every step Popper bind-mounts (shares) a folder from the host (the workspace) into the /workspace folder in the container. Anything written to this folder persists. Conversely, anything that is NOT written in this folder will not persist after the workflow finishes, and the associated containers get destroyed.

Environment variables

A step can define, read, and modify environment variables. A step defines environment variables using the env attribute. For example, you could set the variables FIRST, MIDDLE, and LAST using this:

- uses: "docker://alpine:3.9"
  args: ["sh", "-c", "echo my name is: $FIRST $MIDDLE $LAST"]
    FIRST: "Jane"
    MIDDLE: "Charlotte"
    LAST: "Doe"

When the above step executes, Popper makes these variables available to the container and thus the above prints to the terminal:

my name is: Jane Charlotte Doe

Note that these variables are only visible to the step defining them and any modifications made by the code executed within the step are not persisted between steps (i.e. other steps do not see these modifications).

Git Variables

When Popper executes insides a git repository, it obtains information related to Git. These variables are prefixed with GIT_ (e.g. to GIT_COMMIT or GIT_BRANCH).

Exit codes and statuses

Exit codes are used to communicate about a step’s status. Popper uses the exit code to set the workflow execution status, which can be success, neutral, or failure:

Exit code Status Description
0 success The step completed successfully and other tasks that depends on it can begin.
78 neutral The configuration error exit status (EX_CONFIG) indicates that the step
terminated but did not fail. For example, a filter step can use a neutral status
to stop a workflow if certain conditions aren't met. When a step
returns this exit status, Popper terminates all concurrently running steps and
prevents any future steps from starting. The associated check run shows a
neutral status, and the overall check suite will have a status of success
as long as there were no failed or cancelled steps.
All other failure Any other exit code indicates the step failed. When a step fails, all concurrent
steps are cancelled and future steps are skipped. The check run and
check suite both get a failure status.

Container Engines

By default, Popper workflows run in Docker on the machine where popper run is being executed (i.e. the host machine). This section describes how to execute in other container engines. See next section for information on how to run workflows on resource managers such as SLURM and Kubernetes.

To run workflows on other container engines, an --engine <engine> flag for the popper run command can be given, where <engine> is one of the supported ones. When no value for this flag is given, Popper executes workflows in Docker. Below we briefly describe each container engine supported, and lastly describe how to pass engine-specific configuration options via the --conf flag.


Docker is the default engine used by the popper run. All the container configuration for the docker engine is supported by Popper.


Popper can execute a workflow in systems where Singularity 3.2+ is available. To execute a workflow in Singularity containers:

popper run --engine singularity


  • The use of ARG in Dockerfiles is not supported by Singularity.
  • The --reuse flag of the popper run command is not supported.


There are situations where a container runtime is not available and cannot be installed. In these cases, a step can be executed directly on the host, that is, on the same environment where the popper command is running. This is done by making use of the special sh value for the uses attribute. This value instructs Popper to execute the command or script given in the runs attribute. For example:

- uses: "sh"
  runs: ["ls", "-la"]

- uses: "sh"
  runs: "./path/to/my/"
  args: ["some", "args", "to", "the", "script"]

In the first step above, the ls -la command is executed on the workspace folder (see “The Workspace” section). The second one shows how to execute a script. Note that the command or script specified in the runs attribute are NOT executed in a shell. If you need a shell, you have to explicitly invoke one, for example:

- uses: sh
  runs: [bash, -c, 'sleep 10 && true && exit 0']

The obvious downside of running a step on the host is that, depending on the command being executed, the workflow might not be portable.

Custom engine configuration

Other than bind-mounting the /workspace folder, Popper runs containers with any default configuration provided by the underlying engine. However, a --conf flag is provided by the popper run command to specify custom options for the underlying engine in question (see here for more).

Resource Managers

Popper can execute steps in a workflow through other resource managers like SLURM besides the host machine. The resource manager can be specified either through the --resource-manager/-r option or through the config file. If neither of them are provided, the steps are run in the host machine by default.


Popper workflows can run on HPC (Multi-Node environments) using Slurm as the underlying resource manager to distribute the execution of a step to several nodes. You can get started with running Popper workflows through Slurm by following the example below.

Let’s consider a workflow sample.yml like the one shown below.

- id: one
  uses: docker://alpine:3.9
  args: ["echo", "hello-world"]

- id: two
  uses: popperized/bin/sh@master
  args: ["ls", "-l"]

To run all the steps of the workflow through slurm resource manager, use the --resource-manager or -r option of the popper run subcommand to specify the resource manager.

popper run -f sample.yml -r slurm

To have more finer control on which steps to run through slurm resource manager, the specifications can be provided through the config file as shown below.

We create a config file called config.yml with the following contents.

  name: docker
    privileged: True
    hostname: example.local

  name: slurm
      nodes: 2

Now, we execute popper run with this config file as follows:

popper run -f sample.yml -c config.yml

This runs the step one locally in the host and step two through slurm on 2 nodes.


Popper executes the workflows by default using the host machine as the resource manager. So, when no resource manager is provided like the example below, the workflow runs on the local machine.

popper run -f sample.yml

The above assumes docker as the container engine and host as the resource manager to be used.