> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/connected-analytics/project.md).

# Project

- [Data](https://help.connected.illumina.com/connected-analytics/project/p-data.md)
- [Non-Indexed Folders](https://help.connected.illumina.com/connected-analytics/project/p-data/non-indexed-folders.md)
- [Data Integrity](https://help.connected.illumina.com/connected-analytics/project/p-data/data-integrity.md)
- [Storage Cost Managment](https://help.connected.illumina.com/connected-analytics/project/p-data/storage-cost-managment.md)
- [Data - Troubleshooting](https://help.connected.illumina.com/connected-analytics/project/p-data/data-troubleshooting.md)
- [Samples](https://help.connected.illumina.com/connected-analytics/project/p-samples.md)
- [Activity](https://help.connected.illumina.com/connected-analytics/project/p-activity.md)
- [Flow](https://help.connected.illumina.com/connected-analytics/project/p-flow.md)
- [Reference Data](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-referencedata.md)
- [Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines.md)
- [Nextflow](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-nextflow.md)
- [CWL](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-cwl.md)
- [XML Input Form](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-inputform.md)
- [JSON-Based input forms](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms.md)
- [inputForm.json](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/inputform-json.md)
- [JSON Schema](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/inputform-json/inputform.json-syntax.md)
- [onRender.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onrender.js.md)
- [onSubmit.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onsubmit.js.md)
- [onFinished.js](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/onfinished.js.md)
- [JSON Scatter Gather Pipeline](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/json-based-input-forms/json-scatter-gather-pipeline.md)
- [Git-Sourced Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/git-sourced-pipelines-experimental.md)
- [Basic Git-Sourced Pipeline Example](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/git-sourced-pipelines-experimental/basic-git-sourced-pipeline-example.md)
- [Tips and Tricks](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-pipelines/pi-tips.md)
- [Analyses](https://help.connected.illumina.com/connected-analytics/project/p-flow/f-analyses.md)
- [Base](https://help.connected.illumina.com/connected-analytics/project/p-base.md)
- [Tables](https://help.connected.illumina.com/connected-analytics/project/p-base/base-tables.md)
- [Data Catalogue](https://help.connected.illumina.com/connected-analytics/project/p-base/base-tables/datacatalogue.md)
- [Query](https://help.connected.illumina.com/connected-analytics/project/p-base/base-query.md)
- [Schedule](https://help.connected.illumina.com/connected-analytics/project/p-base/base-schedule.md)
- [Snowflake](https://help.connected.illumina.com/connected-analytics/project/p-base/base-snowflake.md)
- [Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench.md)
- [Workspaces](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces.md)
- [Bench Clusters](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/bench-clusters.md)
- [Sun Grid Engine (SGE) on Platform Core Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/sun-grid-engine-sge-on-ica-bench.md)
- [Spark on Platform Core Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-workspaces/spark-on-ica-bench.md): Running a Spark application in a Bench Spark Cluster
- [JupyterLab](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-jupyterlab.md)
- [Bring Your Own Bench Image](https://help.connected.illumina.com/connected-analytics/project/p-bench/bring-your-own-bench-image.md)
- [Bench Internal Command Line Interface](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-command-line-interface.md)
- [Pipeline Development in Bench (Experimental)](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental.md)
- [Creating a Pipeline from Scratch](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/creating-a-pipeline-from-scratch.md)
- [nf-core Pipelines](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/nf-core-pipelines.md)
- [Updating an Existing Flow Pipeline](https://help.connected.illumina.com/connected-analytics/project/p-bench/pipeline-development-in-bench-experimental/updating-an-existing-flow-pipeline.md)
- [Containers in Bench](https://help.connected.illumina.com/connected-analytics/project/p-bench/containers-in-bench.md)
- [FUSE Driver](https://help.connected.illumina.com/connected-analytics/project/p-bench/bench-fusedriver.md)
- [Run DRAGEN in Bench - Interactive](https://help.connected.illumina.com/connected-analytics/project/p-bench/run-dragen-in-bench-interactive.md)
- [Cohorts](https://help.connected.illumina.com/connected-analytics/project/p-cohorts.md)
- [Create a Cohort](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-create.md)
- [Import New Samples](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-import.md)
- [Prepare Metadata Sheets](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-metadata.md)
- [Precomputed GWAS and PheWAS](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-gwas-phewas.md)
- [Cohort Analysis](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-analysis.md)
- [Compare Cohorts](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-comparison.md)
- [Cohorts Data in Base](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-base.md)
- [Oncology Walk-through](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-walkthrough-cancer.md)
- [Rare Genetic Disorders Walk-through](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-walkthrough-raredisease.md)
- [Public Data Sets](https://help.connected.illumina.com/connected-analytics/project/p-cohorts/cohorts-publicdata.md)
- [Details](https://help.connected.illumina.com/connected-analytics/project/p-details.md)
- [Team](https://help.connected.illumina.com/connected-analytics/project/p-team.md)
- [Connectivity](https://help.connected.illumina.com/connected-analytics/project/p-connectivity.md)
- [Service Connector](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/service-connector.md)
- [Service Connector Troubleshooting](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/service-connector/service-connector-troubleshooting.md)
- [Project Connector](https://help.connected.illumina.com/connected-analytics/project/p-connectivity/project-connector.md)
- [Notifications](https://help.connected.illumina.com/connected-analytics/project/p-notifications.md)


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