Skip to content

docs: Move process directives into separate pages #7454

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
bentsherman wants to merge 1 commit into
base: master
Choose a base branch
from
Draft

docs: Move process directives into separate pages #7454

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
59 changes: 58 additions & 1 deletion .docusaurus_site/sidebars.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,64 @@ module.exports = {
"reference/stdlib-groovy"
]
},
"reference/process",
{
type: "category",
label: "Process",
link: { type: "doc", id: "reference/process" },
items: [
"reference/process/task-properties",
"reference/process/inputs-outputs-typed",
"reference/process/inputs-outputs",
{
type: "category",
label: "Directives",
link: { type: "doc", id: "reference/process/directives" },
items: [
"reference/process/directives/accelerator",
"reference/process/directives/after-script",
"reference/process/directives/arch",
"reference/process/directives/array",
"reference/process/directives/before-script",
"reference/process/directives/cache",
"reference/process/directives/cluster-options",
"reference/process/directives/conda",
"reference/process/directives/container",
"reference/process/directives/container-options",
"reference/process/directives/cpus",
"reference/process/directives/debug",
"reference/process/directives/disk",
"reference/process/directives/error-strategy",
"reference/process/directives/executor",
"reference/process/directives/ext",
"reference/process/directives/fair",
"reference/process/directives/hints",
"reference/process/directives/label",
"reference/process/directives/machine-type",
"reference/process/directives/max-errors",
"reference/process/directives/max-forks",
"reference/process/directives/max-retries",
"reference/process/directives/max-submit-await",
"reference/process/directives/memory",
"reference/process/directives/module",
"reference/process/directives/penv",
"reference/process/directives/pod",
"reference/process/directives/publish-dir",
"reference/process/directives/queue",
"reference/process/directives/resource-labels",
"reference/process/directives/resource-limits",
"reference/process/directives/scratch",
"reference/process/directives/secret",
"reference/process/directives/shell",
"reference/process/directives/spack",
"reference/process/directives/stage-in-mode",
"reference/process/directives/stage-out-mode",
"reference/process/directives/store-dir",
"reference/process/directives/tag",
"reference/process/directives/time"
]
}
]
},
"reference/operator"
]
},
Expand Down
8 changes: 4 additions & 4 deletions docs/aws.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -538,8 +538,8 @@ See [aws][config-aws] to learn more about advanced configuration options.
[config-aws]: ./reference/config/aws
[config-process-selectors]: ./config#process-selectors
[fusion-page]: ./fusion
[process-container]: ./reference/process#container
[process-containerOptions]: ./reference/process#containeroptions
[process-label]: ./reference/process#label
[process-queue]: ./reference/process#queue
[process-container]: ./reference/process/directives/container
[process-containerOptions]: ./reference/process/directives/container-options
[process-label]: ./reference/process/directives/label
[process-queue]: ./reference/process/directives/queue
[wave-page]: ./wave
12 changes: 6 additions & 6 deletions docs/cache-and-resume.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -241,16 +241,16 @@ Nextflow now has a built-in way to compare two task runs. See the [Data lineage]
[cli-clean]: ./reference/cli/clean
[cli-log]: ./reference/cli/log
[operator-join]: ./reference/operator#join
[process-arch]: ./reference/process#arch
[process-cache]: ./reference/process#cache
[process-conda]: ./reference/process#conda
[process-ext]: ./reference/process#ext
[process-arch]: ./reference/process/directives/arch
[process-cache]: ./reference/process/directives/cache
[process-conda]: ./reference/process/directives/conda
[process-ext]: ./reference/process/directives/ext
[process-input]: ./process#inputs
[operator-merge]: ./reference/operator#merge
[process-module]: ./reference/process#module
[process-module]: ./reference/process/directives/module
[process-out-eval]: ./process#eval-output-eval
[process-script]: ./process#script
[process-spack]: ./reference/process#spack
[process-spack]: ./reference/process/directives/spack
[process-stub]: ./process#stub
[stdlib-namespaces-workflow]: ./reference/stdlib-namespaces/workflow
[strict-syntax-page]: ./strict-syntax
Expand Down
2 changes: 1 addition & 1 deletion docs/conda.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -221,4 +221,4 @@ Conda advanced configuration settings are described in the [conda][config-conda]

[config-conda]: ./reference/config/conda
[config-profiles]: ./config#config-profiles
[process-conda]: ./reference/process#conda
[process-conda]: ./reference/process/directives/conda
2 changes: 1 addition & 1 deletion docs/config.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -347,7 +347,7 @@ This approach is useful for handling workflow events without modifying the pipel
[config-options]: ./reference/config
[nxf-env-vars]: ./reference/env-vars#nextflow-settings
[process-reference]: ./reference/process
[process-label]: ./reference/process#label
[process-label]: ./reference/process/directives/label
[secrets-page]: ./secrets
[strict-syntax-page]: ./strict-syntax
[syntax-expressions]: ./reference/syntax#expressions
Expand Down
2 changes: 1 addition & 1 deletion docs/container.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -91,4 +91,4 @@ Nextflow manages the file system mounts for a container to provide task inputs.
[container-singularity]: ./container/singularity
[container-smolvm]: ./container/smolvm
[execution-report-tasks]: ./reports#tasks
[process-container]: ./reference/process#container
[process-container]: ./reference/process/directives/container
2 changes: 1 addition & 1 deletion docs/executor.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,4 +64,4 @@ Use [`process.executor`][process-executor] to set the executor, e.g. `process.ex
[executor-sge]: ./executor/sge
[executor-slurm]: ./executor/slurm
[executor-tcs]: ./executor/tcs
[process-executor]: ./reference/process#executor
[process-executor]: ./reference/process/directives/executor
22 changes: 11 additions & 11 deletions docs/executor/aws-batch.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,14 @@ The following [hints][process-hints] are supported:
See [AWS Batch][aws-batch] for more information.

[aws-batch]: ../aws#aws-batch
[process-accelerator]: ../reference/process#accelerator
[process-arch]: ../reference/process#arch
[process-container]: ../reference/process#container
[process-containeroptions]: ../reference/process#containeroptions
[process-cpus]: ../reference/process#cpus
[process-disk]: ../reference/process#disk
[process-hints]: ../reference/process#hints
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-resourcelabels]: ../reference/process#resourcelabels
[process-time]: ../reference/process#time
[process-accelerator]: ../reference/process/directives/accelerator
[process-arch]: ../reference/process/directives/arch
[process-container]: ../reference/process/directives/container
[process-containeroptions]: ../reference/process/directives/container-options
[process-cpus]: ../reference/process/directives/cpus
[process-disk]: ../reference/process/directives/disk
[process-hints]: ../reference/process/directives/hints
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-resourcelabels]: ../reference/process/directives/resource-labels
[process-time]: ../reference/process/directives/time
18 changes: 9 additions & 9 deletions docs/executor/azure-batch.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,12 @@ Use the following process directives to control resource requests and other job
See [Azure Batch][azure-batch] for more information.

[azure-batch]: ../azure#azure-batch
[process-container]: ../reference/process#container
[process-containeroptions]: ../reference/process#containeroptions
[process-cpus]: ../reference/process#cpus
[process-disk]: ../reference/process#disk
[process-machinetype]: ../reference/process#machinetype
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-resourcelabels]: ../reference/process#resourcelabels
[process-time]: ../reference/process#time
[process-container]: ../reference/process/directives/container
[process-containeroptions]: ../reference/process/directives/container-options
[process-cpus]: ../reference/process/directives/cpus
[process-disk]: ../reference/process/directives/disk
[process-machinetype]: ../reference/process/directives/machine-type
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-resourcelabels]: ../reference/process/directives/resource-labels
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/bridge.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@ Use the following process directives to control resource requests and other job
- [queue][process-queue]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
8 changes: 4 additions & 4 deletions docs/executor/flux.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ By default, Flux sends all output to the `.command.log` file. To send this outpu
Flux does not support the `memory` directive.
:::

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
18 changes: 9 additions & 9 deletions docs/executor/google-batch.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,12 @@ Use the following process directives to control resource requests and other job
See [Cloud Batch][google-batch] for further configuration details.

[google-batch]: ../google#cloud-batch
[process-accelerator]: ../reference/process#accelerator
[process-container]: ../reference/process#container
[process-containeroptions]: ../reference/process#containeroptions
[process-cpus]: ../reference/process#cpus
[process-disk]: ../reference/process#disk
[process-machinetype]: ../reference/process#machinetype
[process-memory]: ../reference/process#memory
[process-resourcelabels]: ../reference/process#resourcelabels
[process-time]: ../reference/process#time
[process-accelerator]: ../reference/process/directives/accelerator
[process-container]: ../reference/process/directives/container
[process-containeroptions]: ../reference/process/directives/container-options
[process-cpus]: ../reference/process/directives/cpus
[process-disk]: ../reference/process/directives/disk
[process-machinetype]: ../reference/process/directives/machine-type
[process-memory]: ../reference/process/directives/memory
[process-resourcelabels]: ../reference/process/directives/resource-labels
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/htcondor.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ Use the following process directives to control resource requests and other job
- [memory][process-memory]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-disk]: ../reference/process#disk
[process-memory]: ../reference/process#memory
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-disk]: ../reference/process/directives/disk
[process-memory]: ../reference/process/directives/memory
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/hyperqueue.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ Use the following process directives to control resource requests and other job
- [memory][process-memory]
- [time][process-time]

[process-accelerator]: ../reference/process#accelerator
[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-time]: ../reference/process#time
[process-accelerator]: ../reference/process/directives/accelerator
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-time]: ../reference/process/directives/time
14 changes: 7 additions & 7 deletions docs/executor/kubernetes.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,10 @@ See [Kubernetes][k8s-page] for how to set up a Kubernetes cluster to run Nextflo

[config-k8s]: ../reference/config/k8s
[k8s-page]: ../kubernetes
[process-accelerator]: ../reference/process#accelerator
[process-cpus]: ../reference/process#cpus
[process-disk]: ../reference/process#disk
[process-memory]: ../reference/process#memory
[process-pod]: ../reference/process#pod
[process-resourcelabels]: ../reference/process#resourcelabels
[process-time]: ../reference/process#time
[process-accelerator]: ../reference/process/directives/accelerator
[process-cpus]: ../reference/process/directives/cpus
[process-disk]: ../reference/process/directives/disk
[process-memory]: ../reference/process/directives/memory
[process-pod]: ../reference/process/directives/pod
[process-resourcelabels]: ../reference/process/directives/resource-labels
[process-time]: ../reference/process/directives/time
12 changes: 6 additions & 6 deletions docs/executor/local.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,9 @@ To run tasks in containers, propagate the device environment variable into the c

[container-docker]: ../container/docker
[container-podman]: ../container/podman
[process-accelerator]: ../reference/process#accelerator
[process-container]: ../reference/process#container
[process-containeroptions]: ../reference/process#containeroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-time]: ../reference/process#time
[process-accelerator]: ../reference/process/directives/accelerator
[process-container]: ../reference/process/directives/container
[process-containeroptions]: ../reference/process/directives/container-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/lsf.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@ Use the following process directives to control resource requests and other job

LSF supports both *per-core* and *per-job* memory limits. Nextflow assumes the *per-core* mode and divides the requested [memory][process-memory] by the number of requested [cpus][process-cpus]. When LSF runs in *per-job* mode, set the `executor.perJobMemLimit` config option. See the [Platform LSF documentation](https://www.ibm.com/support/knowledgecenter/SSETD4_9.1.3/lsf_config_ref/lsf.conf.lsb_job_memlimit.5.dita) for more information.

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/moab.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,8 @@ Use the following process directives to control resource requests and other job
- [queue][process-queue]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/nqsii.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@ Use the following process directives to control resource requests and other job
- [queue][process-queue]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/oar.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@ clusterOptions = [ '-t besteffort', '--project myproject' ]

See [clusterOptions][process-clusteroptions] for details.

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/pbs.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@ Use the following process directives to control resource requests and other job
- [queue][process-queue]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
10 changes: 5 additions & 5 deletions docs/executor/pbspro.mdx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@ Use the following process directives to control resource requests and other job
- [queue][process-queue]
- [time][process-time]

[process-clusteroptions]: ../reference/process#clusteroptions
[process-cpus]: ../reference/process#cpus
[process-memory]: ../reference/process#memory
[process-queue]: ../reference/process#queue
[process-time]: ../reference/process#time
[process-clusteroptions]: ../reference/process/directives/cluster-options
[process-cpus]: ../reference/process/directives/cpus
[process-memory]: ../reference/process/directives/memory
[process-queue]: ../reference/process/directives/queue
[process-time]: ../reference/process/directives/time
Loading
Loading