Difference between revisions of "Nextflow"
Moskalenko (talk | contribs) (Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|nextflow}} |{{#vardefine:url|https://www.nextflow.io/}} <!--CONFIGURATION: OPTIONAL (|1}} means it's O...") |
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:Workflow Automation]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|nextflow}} | |{{#vardefine:app|nextflow}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Nextflow appears to be very sensitive to Lustre quota state. If your group has both a soft and a hard quota on /blue (Burst Quota) then nextflow may start randomly crashing with SIGBUS errors when running out of /blue directories. If you observe such errors reduce your quota usage below the soft limit (the amount paid for) and do not rely on the availability of the burst quota (hard limit). | |
|}} | |}} | ||
Latest revision as of 16:24, 19 August 2022
Description
Data-driven computational pipelines
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.
Environment Modules
Run module spider nextflow to find out what environment modules are available for this application.
System Variables
- HPC_NEXTFLOW_DIR - installation directory
Additional Information
Nextflow appears to be very sensitive to Lustre quota state. If your group has both a soft and a hard quota on /blue (Burst Quota) then nextflow may start randomly crashing with SIGBUS errors when running out of /blue directories. If you observe such errors reduce your quota usage below the soft limit (the amount paid for) and do not rely on the availability of the burst quota (hard limit).