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Running Nextflow Pipelines

This tutorial demonstrates how to use Nextflow pipelines on DNAnexus by importing a Nextflow pipeline from a remote repository or building from local disk space.

A license is required to create a DNAnexus app/applet from the Nextflow script folder. Contact Sales for more information.
This documentation assumes you already have a basic understanding of how to develop and run a Nextflow pipeline. To learn more about Nextflow, visit Nextflow Documentation.
On the DNAnexus Platform you can import or build a Nextflow pipeline as a DNAnexus executable (i.e. app or applet) from a Nextflow pipeline script located from a remote repository or from your local disk space. You can import, build, and run Nextflow pipelines using the graphical user interface (UI) or the command-line interface (CLI).
Quickstart
Pipeline Script Folder Structure
A Nextflow pipeline script is structured as a folder with Nextflow scripts with optional configuration files and subfolders. Below are the basic elements of the folder structure when building a Nextflow executable:
(Required) A main Nextflow file with the extension .nf containing the pipeline. The default filename is main.nf.  A different filename can be specified in the nextflow.config file.
(Optional) A nextflow.config file.
(Optional, recommended) A nextflow_schema.json file. If this file is present at the root folder of the Nextflow script when importing or building the executable, the input parameters described in the file will be exposed as the built Nextflow pipeline applet's input parameters. See this section for more information on how the exposed parameters are used at run time.  
(Optional) Subfolders and other configuration files. Subfolders and other configuration files can be referenced by the main Nextflow file or nextflow.config via theinclude or includeConfig keyword. Ensure that all referenced subfolders and files exist under the pipeline script folder at the time of building or importing the pipeline.
An nf-core flavored folder structure is encouraged but not required.
Importing a Nextflow Pipeline
Import via UI
To import a Nextflow pipeline via the UI, click on the Add button on the top-right corner of the project’s Manage tab, then expand the dropdown menu. Select the Import Pipeline/Workflow option.
Once the Import Pipeline/Workflow modal appears, enter the repository URL where the Nextflow pipeline source code resides, for example, "https://github.com/nextflow-io/hello". Then choose the desired project import location. If the repository is private,  provide the credentials necessary for accessing it.

An example of the Import Pipeline/Workflow modal:
Note that the “Estimated Price” value shown here is only an example. The actual price depends on the pricing model and runtime of the import job.
Once you’ve provided the necessary information, click the Start Import button and the import process will start as a pipeline import job, in the project specified in the Import To field (default is the current project). 
After you've launched the import job, you'll see a status message "External workflow import job started" appear.
You can access information about the pipeline import job in the project’s Monitor tab:
Once the import is complete, you can find the imported pipeline executable as an applet. This is the output of the pipeline import job you previously ran:
You can find the newly created Nextflow pipeline applet - e.g. hello - in the project:
Import via CLI
To import a Nextflow pipeline via the CLI, run the following command to specify the repository’s URL, for example, "https://github.com/nextflow-io/hello". You can also provide optional information, such as a repository tag and an import destination:
$ dx build --nextflow \
  --repository https://github.com/nextflow-io/hello \
  --destination project-xxxx:/applets/hello
​
Started builder job job-aaaa
Created Nextflow pipeline applet-zzzz
dx-toolkit supports Nextflow pipeline applet building starting from version v0.338.0, however, the latest version of dx-toolkit is recommended for use due to improved enhancements and bug fixes. 
This documentation is reflecting features supported in version v0.359.0 or later. 
Your destination project’s billTo feature needs to be enabled for Nextflow pipeline applet building. Contact Sales for more information.
If the Nextflow pipeline is in a private repository, use the option --git-credentials to provide the DNAnexus qualified ID or path of the credential files on the Platform. Read more about this here.
Once the pipeline import job has finished, it will generate a new Nextflow pipeline applet with applet ID applet-zzzz. 
Use dx run -h to get more information about running the applet:
$ dx run project-xxxx:/applets/hello -h
usage: dx run project-xxxx:/applets/hello [-iINPUT_NAME=VALUE ...]
​
Applet: hello
​
hello
​
Inputs:
 Nextflow options
  Nextflow Run Options: [-inextflow_run_opts=(string)]
        Additional run arguments for Nextflow (e.g. -profile docker).
​
  Nextflow Top-level Options: [-inextflow_top_level_opts=(string)]
        Additional top-level options for Nextflow (e.g. -quiet).
​
  Soft Configuration File: [-inextflow_soft_confs=(file) [-inextflow_soft_confs=... [...]]]
        (Optional) One or more nextflow configuration files to be appended to the Nextflow pipeline
        configuration set
​
  Script Parameters File: [-inextflow_params_file=(file)]
        (Optional) A file, in YAML or JSON format, for specifying input parameter values
​
 Advanced Executable Development Options
  Debug Mode: [-idebug=(boolean, default=false)]
        Shows additional information in the job log. If true, the execution log messages from
        Nextflow will also be included.
​
  Resume: [-iresume=(string)]
        Unique ID of the previous session to be resumed. If 'true' or 'last' is provided instead of
        the sessionID, will resume the latest resumable session run by an applet with the same name
        in the current project in the last 6 months.
​
  Preserve Cache: [-ipreserve_cache=(boolean, default=false)]
        Enable storing pipeline cache and local working files to the current project. If true, local
        working files and cache files will be uploaded to the platform, so the current session could
        be resumed in the future
​
Outputs:
  Published files of Nextflow pipeline: [published_files (array:file)]
        Output files published by current Nextflow pipeline and uploaded to the job output
        destination.
Importing a Nextflow Pipeline from a Local Disk
Through the CLI you can also build a Nextflow pipeline applet from a pipeline script folder stored on a local disk. For example, you may have a copy of the nextflow-io/hello pipeline from the Nextflow Github on your local laptop, stored in a directory named hello, which contains the following files:
$ pwd
/path/to/hello
$ ls
LICENSE         README.md       main.nf         nextflow.config
​
The folder structure should follow what is required for a Nextflow pipeline script folder described here. 
Building a Nextflow Pipeline Applet
To build a Nextflow pipeline applet using a locally stored pipeline script, run the following command and specify the path to the folder containing the Nextflow pipeline scripts. You can also provide optional information, such as an import destination:
$ dx build --nextflow /path/to/hello \
  --destination project-xxxx:/applets2/hello
{"id": "applet-yyyy"}
Your destination project’s billTo feature needs to be enabled for Nextflow pipeline applet building. Contact S​ales for more information.
This command will package the Nextflow pipeline script folder as an applet named hello with ID applet-yyyy, and store the applet in the destination project and path project-xxxx:/applets2/hello. If an import destination is not provided, the current working directory will be used.
The dx run​ -h command can be run to see information about this applet, similar to the above example.
A Nextflow pipeline applet will have a type “nextflow” under its metadata . This applet acts like a regular DNAnexus applet object, and can be shared with other DNAnexus users who have access to the project containing the applet.
For advanced information regarding the parameters of dx build --nextflow, run dx build --help in the CLI and find the Nextflow section for all arguments that are supported for building an Nextflow pipeline applet.
Building a Nextflow Pipeline App from a Nextflow Pipeline Applet
You can also build a Nextflow pipeline app from a Nextflow pipeline applet by running the command: dx build --app --from applet-xxxx.
Running a Nextflow Pipeline Executable (App or Applet)
Running a Nextflow Pipeline Executable via UI
You can access a Nextflow pipeline applet from the Manage tab in your project, while the Nextflow pipeline app that you built can be accessed by clicking on the Tools Library option from the Tools tab. Once you click on the applet or app, the Run Analysis tab will be displayed. Fill out the required inputs/outputs and click the Start Analysis button to launch the job.
Running a Nextflow Pipeline Applet via CLI
To run the Nextflow pipeline applet, use dx run applet-xxxx or dx run app-xxxx commands in the CLI and specify your inputs:
$ dx run project-yyyy:applet-xxxx \
  -i debug=false \
  --destination project-xxxx:/path/to/destination/ \
  --brief -y
​
job-bbbb
You can list and see the progress of the Nextflow pipeline job tree, which is structured as a head job with many subjobs, using the following command:
# See subjobs in progress
$ dx find jobs --origin job-bbbb
* hello (done) job-bbbb
│ amy 2023-09-20 14:57:58 (runtime 0:02:03)
├── sayHello (3) (hello:nf_task_entry) (done) job-1111
│   amy 2023-09-20 14:58:57 (runtime 0:00:45)
├── sayHello (1) (hello:nf_task_entry) (done) job-2222
│   amy 2023-09-20 14:58:52 (runtime 0:00:52)
├── sayHello (2) (hello:nf_task_entry) (done) job-3333
│   amy 2023-09-20 14:58:48 (runtime 0:00:53)
└── sayHello (4) (hello:nf_task_entry) (done) job-4444
    amy 2023-09-20 14:58:43 (runtime 0:00:50)
Monitoring Jobs
Each Nextflow pipeline executable run is represented as a job tree with one head job and many subjobs. The head job launches and supervises the entire pipeline execution. Each subjob is responsible for a process in the Nextflow pipeline. You can monitor the progress of the entire pipeline job tree by viewing the status of the subjobs (see example above). 
To monitor the detail log of the head job and the subjobs, you can monitor each job’s DNAnexus log via the UI or the CLI.
On the DNAnexus Platform, jobs are limited to a runtime of 30 days. Jobs running longer than 30 days will be automatically terminated.
Monitoring in the UI
Once your job tree is running, you can go to the Monitor tab to view the status of your job tree. From the Monitor tab, you can view the job log of the head job as well as the subjobs by clicking on the Log link in the row of the desired job. You can also view the costs (when your account has permission) and resource usage of a job.
An example of the log of a head job:
An example of the log of a subjob:
Monitoring in the CLI
From the CLI, you can use the  dx watch command to check the status and view the log of the head job or each subjob.
Monitoring the head job:
# Monitor job in progress
$ dx watch job-bbbb
Watching job job-bbbb. Press Ctrl+C to stop watching.
* hello (done) job-bbbb
  amy 2023-09-20 14:57:58 (runtime 0:02:03)
... [deleted]
2023-09-20 14:58:29 hello STDOUT dxpy/0.358.0 (Linux-5.15.0-1045-aws-x86_64-with-glibc2.29) Python/3.8.10
2023-09-20 14:58:30 hello STDOUT bash running (job ID job-bbbb)
2023-09-20 14:58:31 hello STDOUT =============================================================
2023-09-20 14:58:31 hello STDOUT === NF projectDir   : /home/dnanexus/hello
2023-09-20 14:58:31 hello STDOUT === NF session ID   : 0eac8f92-1216-4fce-99cf-dee6e6b04bc2
2023-09-20 14:58:31 hello STDOUT === NF log file     : dx://project-xxxx:/applets/nextflow-job-bbbb.log
2023-09-20 14:58:31 hello STDOUT === NF command      : nextflow -log nextflow-job-bbbb.log run /home/dnanexus/hello -name job-bbbb
2023-09-20 14:58:31 hello STDOUT === Built with dxpy : 0.358.0
2023-09-20 14:58:31 hello STDOUT =============================================================
2023-09-20 14:58:34 hello STDOUT N E X T F L O W  ~  version 22.10.7
2023-09-20 14:58:35 hello STDOUT Launching `/home/dnanexus/hello/main.nf` [job-bbbb] DSL2 - revision: 1647aefcc7
2023-09-20 14:58:43 hello STDOUT [0a/6a81ca] Submitted process > sayHello (4)
2023-09-20 14:58:48 hello STDOUT [f5/87df8b] Submitted process > sayHello (2)
2023-09-20 14:58:53 hello STDOUT [4b/21374a] Submitted process > sayHello (1)
2023-09-20 14:58:57 hello STDOUT [f6/8c44f5] Submitted process > sayHello (3)
2023-09-20 14:59:51 hello STDOUT Hola world!
2023-09-20 14:59:51 hello STDOUT 
2023-09-20 14:59:51 hello STDOUT Ciao world!
2023-09-20 14:59:51 hello STDOUT 
2023-09-20 15:00:06 hello STDOUT Bonjour world!
2023-09-20 15:00:06 hello STDOUT 
2023-09-20 15:00:06 hello STDOUT Hello world!
2023-09-20 15:00:06 hello STDOUT 
2023-09-20 15:00:07 hello STDOUT === Execution completed — cache and working files will not be resumable
2023-09-20 15:00:07 hello STDOUT === Execution completed — upload nextflow log to job output destination project-xxxx:/applets/
2023-09-20 15:00:09 hello STDOUT Upload nextflow log as file: file-GZ5ffkj071zqZ9Qj22qv097J
2023-09-20 15:00:09 hello STDOUT === Execution succeeded — upload published files to job output destination project-xxxx:/applets/
* hello (done) job-bbbb
  amy 2023-09-20 14:57:58 (runtime 0:02:03)
  Output: -
Monitoring a subjob:
# Monitor job in progress
$ dx watch job-cccc
Watching job job-cccc. Press Ctrl+C to stop watching.
sayHello (1) (hello:nf_task_entry) (done) job-cccc
amy 2023-09-20 14:58:52 (runtime 0:00:52)
... [deleted]
2023-09-20 14:59:28 sayHello (1) STDOUT dxpy/0.358.0 (Linux-5.15.0-1045-aws-x86_64-with-glibc2.29) Python/3.8.10
2023-09-20 14:59:30 sayHello (1) STDOUT bash running (job ID job-cccc)
2023-09-20 14:59:33 sayHello (1) STDOUT file-GZ5ffQj047j3Vq7QX220Q5vQ
2023-09-20 14:59:34 sayHello (1) STDOUT Bonjour world!
2023-09-20 14:59:36 sayHello (1) STDOUT file-GZ5ffVQ047j2QXZ2ZkFx4YxG
2023-09-20 14:59:38 sayHello (1) STDOUT file-GZ5ffX0047j2QXZ2ZkFx4YxK
2023-09-20 14:59:41 sayHello (1) STDOUT file-GZ5ffXQ047jGYZ91x6KG32Jp
2023-09-20 14:59:43 sayHello (1) STDOUT file-GZ5ffY8047jF2PY3609JPBKB
sayHello (1) (hello:nf_task_entry) (done) job-cccc
amy 2023-09-20 14:58:52 (runtime 0:00:52)
Output: exit_code = 0
​
Advanced Options: Running a Nextflow Pipeline Executable (App or Applet)
Nextflow Execution on DNAnexus
The Nextflow pipeline executable is launched as a job tree, with one head job running the Nextflow executor, and multiple subjobs running a single process each. Throughout the pipeline’s execution, the head job remains in “running” state and supervises the job tree’s execution. 
Nextflow Execution Log File
When a Nextflow head job (i.e. job-xxxx) enters its terminal state (i.e. "done" or "failed"), a Nextflow log file with filename as nextflow-<job-xxxx>.log will be written to the destination path of the head job.
Private Docker Repository
DNAnexus supports Docker container engines for the Nextflow pipeline execution environment. The pipeline developer may refer to a public Docker repository or a private one. When the pipeline is referencing a private Docker repository, you should provide your Docker credential file as a file input of docker_creds to the Nextflow pipeline executable when launching the job tree. 
Syntax of a private Docker credential:
{
  "docker_registry": {
    "registry": "url-to-registry",
    "username": "name123",
    "token": "12345678"
  }
}
It is encouraged to save this credential file in a separate project where only limited users have permission to access it for privacy reasons.
Nextflow Pipeline Executable Inputs and Outputs
Specifying Input Values to a Nextflow Pipeline Executable
Below are all possible means that you can specify an input value at build time and runtime. They are listed in order of precedence (items listed first have greater precedence and override items listed further down the list): 
1.Executable (app or applet) run time 
1.DNAnexus Platform app or applet input. 
CLI example: 
dx run project-xxxx:applet-xxxx -i reads_fastqgz=project-xxxx:file-yyyy
reads_fastqgz is an example of an executable input parameter name. All Nextflow pipeline inputs can be configured and exposed by the pipeline developer using an nf-core flavored pipeline schema file (nextflow_schema.json).
When the input parameter is expecting a file, you need to specify the value in a certain format based on the  class of the input parameter.  When the input is of the “file” class, use DNAnexus qualified ID (i.e. absolute path to the file object such as “project-xxxx:file-yyyy”); when the input is of the “string” class, use the DNAnexus URI (“dx://project-xxxx:/path/to/file”). See table below for full descriptions of the formatting of PATHs.
You can use dx run <app(let)> --help to query the class of each input parameter at the app(let) level. In the example code block below, fasta is an input parameter of a file object, while fasta_fai is an input parameter of a string object. You will then use DNAnexus qualifiedID format for fasta, and DNAnexus URI format  for fasta_fai.
The DNAnexus object class of each input parameter is based on the “type” and “format” specified in the pipeline’s nextflow_schema.json, when it exists. See additional documentation here to understand how Nextflow input parameter’s type and format (when applicable) converts to an app or applet’s input class.
It is recommended to always use the app/applet means for specifying input values. The platform validates the input class and existence before the job is created. 
All inputs for a Nextflow pipeline executable are set as “optional” inputs. This allows users to have flexibility to specify input via other means.
2.Nextflow pipeline command line input parameter (i.e. nextflow_pipeline_params). This is an optional "string" class input, available for any Nextflow pipeline executable upon it being built. 
CLI example: 
dx run project-xxxx:applet-xxxx -i nextflow_pipeline_params="--foo=xxxx --bar=yyyy", where "--foo=xxxx --bar=yyyy" corresponds to the "--something value" pattern of Nextflow input specification referenced here.
Because nextflow_pipeline_params is a string type parameter with file-path format, use the DNAnexus URI format when the file is stored on DNAnexus.
3.Nextflow options parameter (i.e. nextflow_run_opts). This is a optional "string" class input, available for any Nextflow pipeline executable upon it being built. 
CLI example: 
dx run project-xxxx:applet-xxxx -i nextflow_run_opts=“-profile test”, where -profile is single-dash prefix parameter that corresponds to the Nextflow run options pattern, specifying a preset input configuration.
4.Nextflow parameter file (i.e. nextflow_params_file). This is a optional "file" class input, available for any Nextflow pipeline executable that is being built. 
CLI example:
dx run project-xxxx:applet-xxxx -i nextflow_params_file=project-xxxx:file-yyyy, where project-xxxx:file-yyyy is the DNAnexus qualified ID of the file being passed to nextflow run -params-file <file>. This corresponds to -params-file  option of nextflow run. 
5.Nextflow soft configuration override file (i.e. nextflow_soft_confs). This is a optional "array:file" class input, available for any Nextflow pipeline executable that is being built.
CLI example: 
dx run project-xxxx:applet-xxxx -i nextflow_soft_confs=project-xxxx:file-1111 -i nextflow_soft_confs=project-xxxx:file-2222, where project-xxxx:file-1111 and project-xxxx:file-2222 are the DNAnexus qualified IDs of the file being passed to nextflow run -c <config-file1> -c <config-file2>. This corresponds to -c option of nextflow run, and the order specified for this array of file input is preserved when passing to the nextflow run execution.
The soft configuration file can be used for assigning default values of configuration scopes (such as process).
It is highly recommended to use nextflow_params_file as a replacement to using nextflow_soft_confs for the use case of specifying parameter values,  especially when running Nextflow DSL2 nf-core pipelines. Read more about this at nf-core documentation. 
2.Pipeline source code: 
1.nextflow_schema.json
Pipeline developers may specify default values of inputs in the nextflow_schema.json file.
If an input parameter is of Nextflow’s string type with file-path format, use DNAnexus URI format when the file is stored on DNAnexus.
2.nextflow.config
Pipeline developers may specify default values of inputs in thenextflow.config file.
Pipeline developers may specify a default profile value using --profile <value>, when building the executable. e.g. dx build --nextflow --profile test.
3.main.nf , sourcecode.nf
Pipeline developers may specify default values of inputs in the Nextflow source code file (*.nf).
If an input parameter is of Nextflow’s string type with file-path format, use the DNAnexus URI format when the file is stored on DNAnexus.
# Query for the class of each input parameter
$ dx run project-yyyy:applet-xxxx --help
usage: dx run project-yyyy:applet-xxxx [-iINPUT_NAME=VALUE ...]
​
Applet: example_applet
​
example_applet
​
Inputs:
…
  fasta: [-ifasta=(file)]
…
​
  fasta_fai: [-ifasta_fai=(string)]
…
​
​
# Assign values of the parameter based on the class of the parameter
$ dx run project-yyyy:applet-xxxx -ifasta=”project-xxxx:file-yyyy” -ifasta_fai=”dx://project-xxxx:/path/to/file”
Formats of PATH to File, Folder, or Wildcards
While you can specify a file input parameter’s value at different places as seen above, the valid PATH format referring to the same file will be different depending on the level (DNAnexus API/CLI level or Nextflow script-level) and the class (file object or string) of the executable’s input parameter. Examples of this are given below.
Scenarios
Valid PATH format
• App or applet input parameter class as file object


• CLI/API level (e.g. dx run --destination PATH)
DNAnexus qualified ID (i.e. absolute path to the file object). 
• E.g. (file):
project-xxxx:file-yyyy,
project-xxxx:/path/to/file
• E.g. (folder):
project-xxxx:/path/to/folder/
•App or applet input parameter class as string


• Nextflow configuration and source code files (e.g. nextflow_schema.json, nextflow.config, main.nf, sourcecode.nf)
DNAnexus URI.
• E.g. (file): 
dx://project-xxxx:/path/to/file
• E.g. (folder):
dx://project-xxxx:/path/to/folder/
• E.g. (wildcard):
dx://project-xxxx:/path/to/wildcard_files
Specifying a Nextflow Job Tree Output Folder
When launching a DNAnexus job, you can specify a job-level output destination (e.g.  project-xxxx:/destination/) using the platform-level optional parameter on the UI or on the CLI. In addition, when there is publishDir specified in the pipeline, each output file will be located at <dx_run_path>/<publishDir>/, where <dx_run_path> is the job-level output destination, and  <publishDir> is the path assigned per Nextflow script’s process. 
Read more detail about the output folder specification and publishDir  here. Find an example on how to construct output paths of an nf-core pipeline job tree at run time from our FAQ. 
Advanced Options: Building a Nextflow Pipeline Executable
Advanced Building and Importing Pipelines
There are additional options for dx build --nextflow:
Options
Class
Description
--profile PROFILE
string
Set default profile for the Nextflow pipeline executable.
--repository REPOSITORY
string
Specifies a Git repository of a Nextflow pipeline. Incompatible with --remote.
--repository-tag TAG
string
Specifies tag for Git repository. Can be used only with --repository.
--git-credentials GIT_CREDENTIALS
file
Git credentials used to access Nextflow pipelines from private Git repositories. Can be used only with --repository. More information about the file syntax can be found here.
Use dx build --help for more information.
Private Nextflow Pipeline Repository
When the Nextflow pipeline to be imported is from a private repository, you must provide a file containing the credential to access the the repository:
providers {
  github {
    user = 'username'
    password = 'ghp_xxxx'
  }
}
To protect the credential, it is encouraged to store this credential file in a separate project, where only you have permission to access.
Nextflow Input Parameter Type Conversion to DNAnexus Executable Input Parameter Class
Based on the input parameter’s type and format (when applicable) defined in the corresponding nextflow_schema.json file, each parameter will be assigned to the corresponding class (ref1, ref2).
From:
Nextflow Input Parameter
(defined at nextflow_schema.json) Type

Format
To:
DNAnexus Input Parameter Class
string
file-path
file
string
directory-path
string
string
path
string
string
NA
string
integer
NA
int
number
NA
float
boolean
NA
boolean
object
NA
hash
File Input as String or File Class
As a pipeline developer, you can specify a file input variable as {“type”:“string”, “format”:“file-path”} or  {“type”:“string”, “format”:“path”}, which will be assign to “file” or “string” class, respectively.  When running the executable, based on the class (file or string) of the executable’s input parameter, you will use a specific PATH format to specify the value. See documentation here for an acceptable PATH format for each class.
Converting a URL path to a String
When converting a  file reference from a URL format (e.g. dx://project-xxxx:/path/to/file of a DNAnexus URI) to a String, you will use the method toUriString(). Method toURI().toString() does not give the same result, as toURI() removes the context ID (e.g. project-xxxx), and toString() removes the scheme (e.g. dx://). More info about the Nextflow methods here.
Managing intermediate files and publishing outputs
Pipeline Output Setting Using output: block and publishDir
All files generated by a Nextflow job tree will be stored in its session’s corresponding workDir (i.e. the path where the temporary results are stored). On DNAnexus, when the Nextflow pipeline job is run with “preserve_cache=true”, the workDir is set at the path: project-xxxx:/.nextflow_cache_db/<session_id>/work/. project-xxxx is the project where the job took place, and you can follow the path to access all preserved temporary results. It is useful to be able to access these results for investigating the detailed pipeline progress, and use them for resuming job runs for pipeline development purposes. More info about workDir is described here.
When the Nextflow pipeline job was run with “preserve_cache=false” (default), temporary files will be stored in the job’s temporary workspace which will be deconstructed upon the head job enters its terminate state (i.e. “done”, “failed”, or “terminated”). Since a lot of these files are intermediate input/output being passed between processes and expected to be cleaned up after the job is completed, running with “preserve_cache=false” will help reduce project storage cost for files that are not of interest, and also save you from remembering to clean up all temporary files.
To save the final results of interest, and to display them as the Nextflow pipeline executable’s output, you can declare output files matching the declaration under the script’s output: block, and use Nextflow’s optional publishDir directive to publish them. 
This will make the published output files as the Nextflow pipeline head job’s output, under the executable’s formally defined placeholder output parameter, published_files, as array:file class. Then the files will be organized under the relative folder structure assigned via publishDir. This works for both “preserve_cache=true” and “preserve_cache=false”. Only the “copy” publish mode is supported on DNAnexus.
Values of publishDir
At pipeline development time, the valid value of publishDir can be:
A local path string , e.g. “publishDir path: ./path/to/nf/publish_dir/”, 
A dynamic string value defined as a pipeline input parameter (e.g. “params.outdir”, where “outdir” is a string-class input), allowing pipeline users to determine parameter values at runtime. For example, “publishDir path: '${params.outdir}/some/dir/'” or './some/dir/${params.outdir}/' or './some/dir/${params.outdir}/some/dir/' . 
When publishDir is defined this way, the user who launches the Nextflow pipeline executable is responsible for constructing the publishDir to be a valid relative path.
Find an example on how to construct output paths for an nf-core pipeline job tree at run time from our FAQ. 
publishDir is NOT supported on DNAnexus when assigned as an absolute path (e.g. /path/to/nf/publish_dir/, which starts at root (/)). If an absolute path is defined for the publishDir, no output files will be generated as the job’s output parameter “published_files”. 
Queue Size Configuration
The  queueSize option is part of Nextflow’s executor configuration. It defines how many tasks the executor will handle in a parallel manner. On DNAnexus, this represents the number of subjobs being created at a time (5 by default) by the Nextflow pipeline executable’s head job. If the pipeline’s executor configuration has a value assigned to queueSize, it will override the default value. If the value exceeds the upper limit (1000) on DNAnexus, the root job will error out. See the Nextflow executor configuration page for examples.
Instance Type Determination
Head job instance type determination
The head job of the job tree defaults to running on instance type mem2_ssd1_v2_x4 in AWS regions and azure:mem2_ssd1_x4 in Azure regions. It is possible for users to change to a different instance type than the default, but is not recommended. The head job executes and monitors the subjobs. Changing the instance type for the head job will not affect the computing resources available for subjobs, where most of the heavy computation takes place (see below where to configure instance types for Nextflow processes). Changing the instance type for the head job may be necessary only if it is running out of memory or disk space when staging input files, collecting pipeline output files, or uploading pipeline output files to the project. 
Subjob instance type determination
Each subjob’s instance type is determined based on the profile information provided in the Nextflow pipeline script. You can specify required instances by instance type name via Nextflow’s machineType directive (example below), or using a set of system requirements (e.g. cpus, memory, disk, etc.) according to the official Nextflow documentation. The executor will choose the corresponding instance type that matches the minimal requirement of what is described in the Nextflow pipeline profile using the following logic:
1.Choose the cheapest instance that satisfies the system requirements.
2.Use only SSD type instances.
3.For all things equal (price and instance specifications), it will prefer a version2 (v2) instance type. 
Order of precedence for subjob  instance type determination: 
1.The value assigned to machineType directive.
2.Values assigned to cpus, memory, and disk directives in their configuration.
An example command for specifying machineType by DNAnexus instance type name is provided below:
process foo {
  machineType 'mem1_ssd1_v2_x36'
​
  """
  <your script here>
  """
}
In addition to being used for instance type determination, values assigned to cpus, memory, and disk directives can also be recalled by Nextflow's process implicit variables of task object (e.g. ${task.cpus},  ${task.memory}, ${task.disk}) at runtime for task allocation. 
It is possible the actual selected instance type’s CPUs, memory, or disk capacity being inconsistent with what is allocated by task. The former follows above precedence to determine the instance type, the latter is returning the value assigned in the configuration file.
When using Docker as the runtime container, Nextflow executor is propagating task execution settings to the Docker run command. For example, if task.memory is specified, this would then be the maximum amount of memory the container is allowed to use, for example: docker run --memory ${task.memory}
Nextflow Resume
Preserve Run Caches and Resuming Previous Jobs
Nextflow’s resume feature enables skipping the processes that have been finished successfully and cached in previous runs. The new run can directly jump to downstream processes without needing to start from the beginning of the pipeline. By retrieving cached progress, Nextflow resume helps pipeline developers to save both time and compute costs. It is helpful for testing and troubleshooting when building and developing a Nextflow pipeline.
Nextflow utilizes a scratch storage area for caching and preserving each task’s temporary results. The directory is called “working directory”, and the directory’s path is defined by
The session id, a universally unique identifier (UUID) associated with current execution
Each task’s unique hash ID: a hash number composed of each task’s input values, input files, command line strings, container ID (e.g. Docker image), conda environment, environment modules, and executed scripts in the bin directory, when applicable.
You can utilize the Nextflow resume feature with the following Nextflow pipeline executable parameters:
preserve_cache Boolean type. Default value is false. When set to true, the run will be cached in the current project for future resumes. For example:
dx run applet-xxxx -i reads_fastqgz=project-xxxx:file-yyyy -i preserve_cache=true
This enables the Nextflow job tree to preserve cached information as well as all temporary results in the project where it is executed under the following paths, based on its session ID and each subjob’s unique ID.
The session's cache directory containing information on the location of the workDir, the session progress, etc. are saved to project-xxxx:/.nextflow_cache_db/<session_id>/cache.tar
, where project-xxxx is the project where the job tree is executed.
Each task's working directory will be saved to project-xxxx:/.nextflow_cache_db/<session_id>/work/<2digit>/<30characters>/
, where <2digit>/<30characters>/ is technically the task’s unique ID, and project-xxxx is the project where the job tree is executed.
resume String type. Default value is an empty string, and the run will start from scratch. When assigned with a session id, the run will resume from what is cached for the session id on the project. When assigned with “true” or “last”, the run will determine the session id that corresponds to the latest valid execution in the current project and resume the run from it. For example:
dx run applet-xxxxm -i reads_fastqgz=“project-xxxx:file-yyyy” -i resume="<session_id>”
When preserve_cache=true, DNAnexus executor overrides the value of workDir of the job tree to be project-xxxx:/.nextflow_cache_db/<session_id>/work/, where project-xxxx is the project where the job tree was executed.
When a new job is launched and resumes a cached session (session_id may be formatted as 12345678-1234-1234-1234-123456789012 for example), the new job not only resumes from where the cache left at, but also shares the same session_id with the cached session it resumes. When a new job makes progress in a session and if the job is being cached, it creates temporary results to the same session’s workDir. This will generate a new cache directory (cache.tar) with the latest cache information.
You can have many Nextflow job trees sharing the same sessionID and writing to the same path for workDir and creating its own cache.tar, while only the latest job that ends in “done” or “failed” state will be preserved on the project.
When the head job enters its terminal state (e.g. “failed” or “terminated”) that is not caused by the executor, no cache directory will be preserved, even when the job was run with preserve_cache=true. Subsequent new jobs will not be able to resume from this job run. Examples: a job tree fails due to exceeding a cost limit; a user terminates a job of the job tree, etc.
Below are four possible scenarios and the recommended use cases for –i resume:
Scenarios
Parameters
Use Cases
Note
1
(default)
resume=“” (empty string) and preserve_cache=false
Production data processing;
most high volume use cases


2
resume=“” (empty string) and preserve_cache=true
Pipeline development;
only happens for the first few pipeline tests.


During development; it would be useful to see all intermediate results in workDir.
Only up to 20 Nextflow sessions can be preserved per project.
3
resume=<session_ID>|“true”|“last”and preserve_cache=false
Pipeline development;
pipeline developers can investigate the job workspace with --delay_workspace_destruction and --ssh


4
resume=<session_ID>|“true”|“last” and preserve_cache=true
Pipeline development;
only happens for the first few tests.
Only 1 job with the same <session_ID> can run at each time point.
Cache Preserve Limitations and Cleaning Up workDir
It is a good practice to frequently clean up the workDir to save on storage costs. The maximum number of sessions that can be preserved in a DNAnexus project is 20 sessions. If you exceed the limit, the job will generate an error with the following message: 
“The number of preserved sessions is already at the limit (N=20) and preserve_cache is true. Please remove the folders in <project-id>:/.nextflow_cache_db/ to be under the limit, if you want to preserve the cache of this run. “ 
To clean up all preserved sessions under a project, you can delete the entire ./nextflow_cache_db folder. To clean up a specific session’s cached folder, you can delete the specific .nextflow_cache_db/<session_id>/ folder. To delete a folder in UI, you can follow the documentation on deleting objects. To delete a folder in CLI, you can run:
dx rm -r project-xxxx:/.nextflow_cache_db/              # cleanup ALL sessions caches
dx rm -r project-xxxx:/.nextflow_cache_db/<session_id>/ # clean up a specific session’s cache
Note that deleting an object on UI or using CLI dx rm cannot be undone. Once the session work directory is deleted or moved, subsequent runs will not be able to resume from the session.
For each session, only one job is allowed to resume the session’s cached results, and preserve its own progress to this session. There is no limit if multiple jobs resume and preserve multiple different sessions, as long as each job is preserving a different session. There is also no limit for multiple jobs to resume the same session, as long as only one or none is preserving the progress to the session.
Nextflow’s errorStrategy
Nextflow’s errorStrategy directive allows you to define how the error condition is managed by the Nextflow executor at the process level. When an error status is returned, by default, the process and other pending processes stop immediately (i.e. errorStrategy terminate), and this in turn forces the entire pipeline execution to be terminated. 
There are four error strategy options of Nextflow executor: terminate, finish, ignore, and retry. Below is a table of behaviors for each strategy. Note that "all other subjobs" in the third column have not yet entered their terminal states.

errorStrategy
Subjob Error
Head Job
All Other Subjobs
terminate
Job properties set with: "nextflow_errorStrategy”:"terminate”,
"nextflow_errored_subjob”:"self”


End in “failed” state immediately
Job properties set with:
"nextflow_errorStrategy”:”terminate”, 
"nextflow_errored_subjob”:”job-xxxx",
"nextflow_terminated_subjob”:”job-yyyy, job-zzzz"
, where job-xxxx is the errored subjob, and job-yyyy is the other subjobs that were terminated due to this error.


End in “failed” state immediately, with error message, “Job was terminated by Nextflow with terminate errorStrategy for job-xxxx, check the job log to find the failure”
End in “failed” state immediately.
finish
Job properties set with: 
"nextflow_errorStrategy”:"finish”,
"nextflow_errored_subjob”:"self”


End in “done” state immediately
Job properties set with: 
"nextflow_errorStrategy:finish”,
"nextflow_errored_subjob”:”job-xxxx, job-2xxx"
, where job-xxxx and job-2xxxx are the the errored subjobs,


Not create new subjobs after the time point of error


End in “failed” state eventually, after other existing subjobs enter their terminal states, with error message “Job was ended with finish errorStrategy for job-xxxx, check the job log to find the failure.”.
Keep on running until entering their terminal states.


If error occurs in any of these subjobs (e.g. job-2xxx), finish errorStrategy will be applied to the subjob because a finish errorStrategy was hit first, ignoring any other error strategies set in the pipeline’s source code or configuration,  as Nextflow’s default behavior.
retry
Job properties set with: 
"nextflow_errorStrategy”:”retry”,
"nex
tflow_errored_subjob”:”self"


End in “done” state immediately
Spin off a new subjob which retries the errored job, with the following job name:
<name> (retry: <RetryCount>) , where <name> is the original subjob name and <RetryCount> is the order of this retry (ex. retry:1, retry:2).


End in a terminal state depending on the terminal states of other currently existing subjobs that are not yet in their terminal states. Can be either “done”, “failed” or “terminated”.
Keep on running until enter their terminal states.


If error occurs in one of these subjobs, their errorStrategy set in the subjob’s corresponding Nextflow process is applied.
ignore
Job properties set with:
"nextflow_errorStrategy”:”ignore”,
"nextflow_errored_subjob”:”self"


End in “done” state immediately
Have job properties set with:
"nextflow_erorrStrategy”:”ignore”,
"nextflow_errorred_subjob”:”job-1xxx, job-2xxx"


Shows “subjob(s) <job-1xxxx>, <job-2xxxx> runs into Nextflow process errors’ ignore errorStrategy were applied” in the end of the job log.


End in a terminal state depending on the terminal states of other currently existing subjobs that are not yet in their terminal states. Can be either “done”, “failed” or “terminated”.
Keep on running until they enter their terminal states.


If error occurs in one of these subjobs, their errorStrategy set in the subjob’s corresponding Nextflow process is applied.

When more than one errorStrategy directives are applied to a pipeline job tree, the following rules will be applied depending on the first errorStrategy used. 
When terminate is the first errorStrategy directive to be triggered in a subjob, all the other ongoing subjobs will result in the "failed" state immediately.
When finish is the first errorStrategy directive to be triggered in a subjob, any other errorStrategy that is reached in the remaining ongoing subjob(s) will also apply the finish errorStrategy, ignoring any other error stategies set in the pipeline’s source code or configuration.
If the retry errorStrategy is the first directive triggered in a subjob, if any of the remaining subjobs trigger a terminate, finish, or ignore errorStrategy, these other errorStrategy directives will be applied to the corresponding subjob.
When  ignore is the first errorStrategy directive to trigger in a subjob , and if any of terminate, finish, or retry errorStrategy directives applies to the remaining subjob(s), that other errorStrategy will be applied to the corresponding subjob.
Independent from Nextflow process-level error conditions, when a Nextflow subjob encounters platform-related restartable errors, such as "ExecutionError", "UnresponsiveWorker", "JMInternalError", "AppInternalError", or "JobTimeoutExceeded", the subjob will follow the executionPolicy determined to the subjob and and restart itself. It will not restart from the head job.
FAQ
My Nextflow job tree failed, how do I find where the errors are?
A: You can find the errored subjob’s job ID from the head job’s nextflow_errored_subjob and nextflow_errorStrategy properties to investigate which subjob failed and which errorStrategy was applied. To query these errorStrategy related properties in CLI, you can run the following command:
$ dx describe job-xxxx --json | jq -r .properties.nextflow_errored_subjob
job-yyyy
$ dx describe job-xxxx --json | jq -r .properties.nextflow_errorStrategy
terminate
where job-xxxx is the head job’s job ID. 

Once you find the errored subjob, you can investigate the job log using the Monitor page by accessing the URL "https:/platform.dnanexus.com/projects/<projectID>/monitor/job/<jobID>", where jobID is the subjob's ID (e.g. job-yyyy), or watch the job log in CLI using dx watch job-yyyy.
If you have the preserve_cache value set to true when start running the Nextflow pipeline executable, you can trace the cache workDir (e.g. project-xxxx:/.nextflow_cache_db/<session_id>/work/) and investigate the intermediate results of this run.   
What is the version of Nextflow that is used? 
A: You can find the Nextflow version used by reading the log of the head job. Each built Nextflow executable is locked down to the specific version of Nextflow executor. 
What container runtimes are supported? 
A: DNAnexus supports Docker as the container runtime for Nextflow pipeline applets. It is recommended to set docker.enabled=true in the Nextflow pipeline configuration, which enables the built Nextflow pipeline applet to execute the pipeline using Docker. 
My job hangs at the end of the analysis. What can I do to avoid this problem? 
A: There can be many possibilities causing the head job to hang.  One of the known reasons is caused by the trace report file being written directly to a DNAnexus URI (e.g. dx://project-xxxx:/path/to/file). To avoid this cause, we suggest you to specify ​​-with-trace path/to/tracefile (using a local path string) to the Nextflow pipeline applet’s nextflow_run_opts input parameter.
Can I have an example of how to construct an output path when I run a Nextflow pipeline with params.outdir, publishDir and job-level destination?
Taking nf-core/sarek (3.3.1) as an example, start with reading the pipeline's logic:
1.The pipeline's publishDir is constructed with a prefix of the params.outdir variable followed by each task's name for each subfolder:
publishDir = [ path: { "${params.outdir}/${...}" }, ... ]
2.params.outdir is a required input parameter to the pipeline, and the default value ofparams.outdir is null. The user running the corresponding Nextflow pipeline executable must specify a value to params.outdir which will:
1.Meet the input requirement for executing the pipeline.
2.Resolve the value ofpublishDir, with outdir as the leading path and each task's name as the subfolder name.
To specify a value of params.outdir for the Nextflow pipeline executable built from the nf-core/sarek pipeline script, you can use the following command:
dx run project-xxxx:applet-zzzz \
-i outdir=./local/to/outdir \   # assign "./local/to/outdir" params.outdir
--brief -y
You can also set a job tree's output destination using --destination :
dx run project-xxxx:applet-zzzz \
-i outdir=./local/to/outdir \   # assign "./local/to/outdir" params.outdir
--destination project-xxxx:/path/to/jobtree/destination/ \ 
--brief -y
This above command will construct the final output paths in the following manner:
1.project-xxxx:/path/to/jobtree/destination/ as the destination of the job tree's shared output folder.
2.project-xxxx:/path/to/jobtree/destination/local/to/outdir as the shared output folder of the all tasks/processes/subjobs of this pipeline.
3.project-xxxx:/path/to/jobtree/destination/local/to/outdir/<task_name> as the output folder of each specific task/process/subjob of this pipeline.
1.This example is built based on Specifying A Nextflow Job Tree Output Folder and Managing intermediate files and publishing outputs.
2.Not all Nextflow pipelines haveparams.outdir as input, nor do all of them use params.outdir in publishDir. Read the source script of the Nextflow pipeline for the actual context of usage and requirements forparams.outdir andpublishDir.

Running Workflows

Running Batch Jobs

Last modified 1mo ago

Scenarios	Valid PATH format
• App or applet input parameter class as file object • CLI/API level (e.g. `dx run --destination PATH`)	DNAnexus qualified ID (i.e. absolute path to the file object). • E.g. (file): `project-xxxx:file-yyyy`, `project-xxxx:/path/to/file` • E.g. (folder): `project-xxxx:/path/to/folder/`
•App or applet input parameter class as string • Nextflow configuration and source code files (e.g. `nextflow_schema.json`, `nextflow.config`, `main.nf`, `sourcecode.nf`)	DNAnexus URI. • E.g. (file): `dx://project-xxxx:/path/to/file` • E.g. (folder): `dx://project-xxxx:/path/to/folder/` • E.g. (wildcard): `dx://project-xxxx:/path/to/wildcard_files`

Options	Class	Description
`--profile PROFILE`	string	Set default profile for the Nextflow pipeline executable.
`--repository REPOSITORY`	string	Specifies a Git repository of a Nextflow pipeline. Incompatible with `--remote`.
`--repository-tag TAG`	string	Specifies tag for Git repository. Can be used only with `--repository`.
`--git-credentials GIT_CREDENTIALS`	file	Git credentials used to access Nextflow pipelines from private Git repositories. Can be used only with `--repository`. More information about the file syntax can be found here.

Scenarios	Parameters	Use Cases	Note
1 (default)	`resume`=“” (empty string) and `preserve_cache=false`	Production data processing; most high volume use cases
2	`resume`=“” (empty string) and `preserve_cache=true`	Pipeline development; only happens for the first few pipeline tests. During development; it would be useful to see all intermediate results in `workDir`.	Only up to 20 Nextflow sessions can be preserved per project.
3	`resume=<session_ID>\|“true”\|“last”`and `preserve_cache=false`	Pipeline development; pipeline developers can investigate the job workspace with `--delay_workspace_destruction` and `--ssh`
4	`resume=<session_ID>\|“true”\|“last”` and `preserve_cache=true`	Pipeline development; only happens for the first few tests.	Only 1 job with the same `<session_ID>` can run at each time point.

`errorStrategy`	Subjob Error	Head Job	All Other Subjobs
`terminate`	Job properties set with: `"nextflow_errorStrategy”:"terminate”, "nextflow_errored_subjob”:"self”` End in “failed” state immediately	Job properties set with: "nextflow_errorStrategy”:”terminate”, "nextflow_errored_subjob”:”job-xxxx", "nextflow_terminated_subjob”:”job-yyyy, job-zzzz" , where `job-xxxx` is the errored subjob, and `job-yyyy` is the other subjobs that were terminated due to this error. End in “failed” state immediately, with error message, “Job was terminated by Nextflow with `terminate` errorStrategy for `job-xxxx`, check the job log to find the failure”	End in “failed” state immediately.
finish	Job properties set with: `"nextflow_errorStrategy”:"finish”, "nextflow_errored_subjob”:"self”` End in “done” state immediately	Job properties set with: `"nextflow_errorStrategy:finish”, "nextflow_errored_subjob”:”job-xxxx, job-2xxx"` , where `job-xxxx` and `job-2xxxx` are the the errored subjobs, Not create new subjobs after the time point of error End in “failed” state eventually, after other existing subjobs enter their terminal states, with error message “Job was ended with finish errorStrategy for job-xxxx, check the job log to find the failure.”.	Keep on running until entering their terminal states. If error occurs in any of these subjobs (e.g. job-2xxx), `finish` `errorStrategy` will be applied to the subjob because a `finish` `errorStrategy` was hit first, ignoring any other error strategies set in the pipeline’s source code or configuration, as Nextflow’s default behavior.
`retry`	Job properties set with: `"nextflow_errorStrategy”:”retry”`, "nex tflow_errored_subjob”:”self" End in “done” state immediately	Spin off a new subjob which retries the errored job, with the following job name: <name> (retry: <RetryCount>) , where <name> is the original subjob name and <RetryCount> is the order of this retry (ex. retry:1, retry:2). End in a terminal state depending on the terminal states of other currently existing subjobs that are not yet in their terminal states. Can be either “done”, “failed” or “terminated”.	Keep on running until enter their terminal states. If error occurs in one of these subjobs, their `errorStrategy` set in the subjob’s corresponding Nextflow process is applied.
`ignore`	Job properties set with: "`nextflow_errorStrategy`”:`”ignore”, "nextflow_errored_subjob”:”self"` End in “done” state immediately	Have job properties set with: `"nextflow_erorrStrategy”:”ignore”, "nextflow_errorred_subjob”:”job-1xxx, job-2xxx"` Shows “subjob(s) <job-1xxxx>, <job-2xxxx> runs into Nextflow process errors’ ignore errorStrategy were applied” in the end of the job log. End in a terminal state depending on the terminal states of other currently existing subjobs that are not yet in their terminal states. Can be either “done”, “failed” or “terminated”.	Keep on running until they enter their terminal states. If error occurs in one of these subjobs, their `errorStrategy` set in the subjob’s corresponding Nextflow process is applied.

From: Nextflow Input Parameter (defined at `nextflow_schema.json`) Type	Format	To: DNAnexus Input Parameter Class
string	file-path	file
string	directory-path	string
string	path	string
string	NA	string
integer	NA	int
number	NA	float
boolean	NA	boolean
object	NA	hash