> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/connected-analytics/api-access/api-concepts/nextflow-pipelines-with-custom-input.md).

# Nextflow Pipelines with Custom Input

## Starting a Nextflow Pipeline with Custom Input

The API call `POST /api/projects/{projectId}/analysis:nextflowWithCustomInput` triggers the execution of a Nextflow pipeline with a custom input in YAML or JSON format, bypassing all input forms typically required by the pipeline. The input will directly provide all necessary data for the pipeline, overriding the default form-based input collection.

### Details

#### URL Parameters

* **projectId** (required): The unique identifier of the project where the pipeline is located. This parameter must be provided in the URL.

#### Request Body

* The request body must contain the input that will be passed to the pipeline, overriding any default inputs.

#### Fields in analysisInput:

* **customInput** (required): A JSON/YAML object containing all the input data which the pipeline requires. The structure and content of the input depend on the specific pipeline, but should follow the expected format defined by the pipeline's logic. The custom input consists of a simple Map structure. These are key and value pairs used in your main.nf.

#### Considerations

* **Input Validation**: Ensure that all required fields for the pipeline are included in the inputJson object. If any critical input is missing or incorrect, the pipeline will not run successfully.
* **Pipeline-Specific Fields**: The structure and names of the fields in inputJson will vary depending on the pipeline. Refer to your pipeline documentation for specific details about the expected inputs.
* **Supported inputs**:
  * **External S3 storage** : individual **files** (filename as last part of the S3 URL) with a maximum of 10,000 files per request. (For folders or more than 10.000 files, use your [own S3 storage](/connected-analytics/web-ui-access/h-storage/s-awss3.md))
  * **Your own S3 storage**, configured as described [here](/connected-analytics/web-ui-access/h-storage/s-awss3.md) : supports both **files** and **folders**.
  * **HTTP(S)** : individual **files** (last part of the url).
  * **BaseSpace** : **files** and **folders** (as BaseSpace data reference identifiers).

### Example

#### main.nf

```
params.in = "test.test"
inputFile = file(params.txts[0])
 
println "maxagesum= $params.maxagesum"
println "ttt= $params.ttt"
println "txts= $params.txts"
println "notallowedcondition= $params.notallowedcondition"
println "group= $params.group"
 
for (groupinstance in params.group) {
    println "groupinstance= $groupinstance"
    println "groupinstance.info= $groupinstance.info"
    for (infoinstance in groupinstance.info) {
      println "infoinstance= $infoinstance"
      infofile = file(infoinstance)
      println "info file ===> name= ${infofile.getName()} uri= ${infofile.toUriString()} size= ${infofile.size()}"
 
    }
}
 
process writetooutput {
        input:
        file x from inputFile
 
        publishDir 'out', pattern: 'out/*', mode: 'move'
        output:
        path 'out/*'
        script:
        """
        #!/bin/bash
        printf "\n maxagesum was "
        printf '${params.maxagesum}'
        printf "\n ttt was "
        printf '${params.ttt}'
        printf "\n txts was "
        printf '${params.txts}'
        printf "\n notallowedcondition was "
        printf '${params.notallowedcondition}'
        printf "\n group was "
        printf '${params.group}'
 
        printf "\n "
        for ((n=0;n<3;n++))
        do
            date +"%H:%M:%S"
            sleep 10
        done
        printf in
        printf "create dir"
        mkdir out
        printf "copy start"
        cp $x out
        printf "copy done"
        """
}
```

#### Example string

To be provided with the request. The unescaped JSON is provided for legibility.

{% tabs %}
{% tab title="JSON" %}
{% code overflow="wrap" %}

```json
"{\"maxagesum\":null,\"ttt\":[\"test\"],\"txts\":[\"dummy.txt\"],\"notallowedcondition\":null,\"notallowedrole\":null,\"group\":[{\"role\":\"c\",\"conditions\":[\"1cancer\",\"covid1\"],\"age\":111,\"info\":[\"test.csv\"]},{\"role\":\"f\",\"conditions\":[\"cancer22\",\"covewd2\"],\"age\":null,\"info\":[\"test.csv\"]}]}"
```

{% endcode %}
{% endtab %}

{% tab title="Unescaped JSON" %}

```yaml
{
  "maxagesum":
     null,
  "ttt": [
    "test"
  ],
  "txts": [
    "dummy.txt"
  ],
  "group": [
    {
      "role": "c",
      "conditions": [
        "1cancer",
        "covid1"
      ],
      "age": 111,
      "info": [
        "test.csv"
      ]
    },
    {
      "role": "f",
      "conditions": [
        "cancer22",
        "covewd2"
      ],
      "info": [
        "test.csv"
      ]
    }
  ]
}
```

{% endtab %}

{% tab title="YAML" %}

```yaml
maxagesum: null
ttt:
  - test
txts:
  - dummy.txt
notallowedcondition: null
notallowedrole: null
group:
  - role: c
    conditions:
      - 1cancer
      - covid1
    age: 111
    info:
      - test.csv
  - role: f
    conditions:
      - cancer22
      - covewd2
    age: null
    info:
      - test.csv
```

{% endtab %}
{% endtabs %}

#### Request Body

```json
{
  "userReference": "string",
  "pipelineId": "string",
  "tags": {
    "technicalTags": [
      "string"
    ],
    "userTags": [
      "string"
    ],
    "referenceTags": [
      "string"
    ]
  },
  "analysisStorageId": "3fa85f64-5717-4562-b3fc-2c963f66afa6",
  "outputParentFolderId": "string",
  "analysisOutput": [
    {
      "sourcePath": "string",
      "type": "FILE",
      "targetProjectId": "string",
      "targetPath": "string",
      "actionOnExist": "string"
    }
  ],
  "analysisInput": {
    "customInput": "string",
    "dataIds": [
      "string"
    ],
    "mounts": [
      {
        "dataId": "string",
        "mountPath": "string"
      }
    ],
    "externalData": [
      {
        "url": "string",
        "type": "string",
        "mountPath": "string",
        "s3Details": {
          "storageCredentialsId": "3fa85f64-5717-4562-b3fc-2c963f66afa6"
        },
        "basespaceDetails": {
          "workgroupId": "string",
          "extensions": "string",
          "pathPrefix": "string"
        }
      }
    ]
  }
}
```


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