Commit 852122be authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Update readme

parent 01dae0ad
Pipeline #7344 passed with stages
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......@@ -24,18 +24,23 @@ Cloud Compatibility
-------------------
This pipeline is also capable of being run on AWS. To do so:
* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
* Edit one of the aws configs in workflow/config/
* In the aws configs in `workflow/configs/`:
* Replace workDir with the S3 bucket generated
* Change region if different
* Change queue to the aws batch queue generated
* In the ondemand and spot configs in `workflow/config/`:
* Change queue to the aws batch queues generated
* The user must be have awscli configured with an appropriate authentication (with ```aws configure``` and access keys) in the environment which nextflow will be run
* Add ```-profile ``` with the name aws config which was custamized
* eg. ```nextflow run workflow/main.nf -profile aws_ondemand```
* Add ```-profile ``` with aws and the queue config which was customized
* eg. ```nextflow run workflow/main.nf -profile aws,ondemand```
To Run:
-------
* Available parameters:
* **-profile**
* what environments to run on, available: `biohpc`, `local`, `cluster`, `aws`, `ondemand`, `spot`
* eg: **-profile biohpc,cluster** to run on BioHPC in cluster mode
* eg: **-profile aws,ondemand** to run on AWS on a on-demand queue
* **--name**
* run name, puts outputs in a directory with this name
* eg: **--name 'test'**
......@@ -58,7 +63,7 @@ To Run:
* eg: ```--outDir 'test'```
* FULL EXAMPLE:
```
nextflow run workflow/main.nf --name 'test' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'
nextflow run workflow/main.nf -profile biohpc,cluster --name 'test' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'
```
* Design example:
......
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