> For the complete documentation index, see [llms.txt](https://help.fovus.co/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.fovus.co/docs/pipeline/miniwdl/miniwdl-submission/prepare-inputs.md).

# Prepare inputs and configure WDL

Upload large shared inputs to Fovus Storage and configure inputs.json and runtime{} with Fovus Tokens before submitting.

This page covers two preparation steps: uploading large shared inputs to Fovus Storage so every task can read them efficiently, and configuring `inputs.json` and `runtime{}` with Fovus Tokens.

See [Pipeline overview](/docs/pipeline/pipeline-overview.md) for how Pipelines differ from Jobs and when to choose a workflow manager.

## Upload large input files

Large shared inputs — reference genomes, shared datasets — should live under the storage mount point before you run the pipeline (`/fovus-storage/pipelines` by default for `miniwdl-fovus run`, or wherever you mounted storage when [driving miniwdl directly](/docs/pipeline/miniwdl/miniwdl-submission/local-manager.md)). Upload once to this folder and every task reads the same path, avoiding a per-task copy of multi-gigabyte files.

Small files (scripts, sample sheets, params) can ship alongside the WDL and pass through `inputs.json` without a separate upload step.

{% columns %}
{% column %}
**Upload to the storage mount when:**

* The file is large
* Many tasks read the same path
* Copying into every task's working directory would waste I/O
  {% endcolumn %}

{% column %}
**Skip a separate upload when:**

* Files are small
* You only need paths already under the storage mount
  {% endcolumn %}
  {% endcolumns %}

For large files, avoid `remoteInputsForAllTasks` — it copies into every task working directory. Pre-stage once under the storage mount instead. See [remoteInputsForAllTasks](/docs/pipeline/miniwdl/miniwdl-config-reference.md) in the config reference for the small-file case.

{% tabs %}
{% tab title="Fovus CLI" %}

```bash
fovus pipeline upload LOCAL_PATH [FOVUS_PATH]
```

* `LOCAL_PATH` — local file or folder to upload
* `FOVUS_PATH` — optional relative path under the storage mount

Example:

```bash
fovus pipeline upload /data/genome-data/ genome-data/
```

Files are available at `/fovus-storage/pipelines/genome-data/`.
{% endtab %}

{% tab title="Mounted storage" %}
If [Fovus Storage is mounted locally](/docs/storage/mount-storage-locally.md), copy files using any standard tool:

```bash
cp -r /data/genome-data/ /fovus-storage/pipelines/genome-data/
```

Or with `rsync` if available:

```bash
rsync -avh /data/genome-data/ /fovus-storage/pipelines/genome-data/
```

{% endtab %}
{% endtabs %}

### To use uploaded files in your workflow

Treat files under the storage mount like any path on Fovus Storage — pass the absolute path in through a `File` input:

```json
{
  "align.ref": "/fovus-storage/pipelines/genome-data/GRCh38.fa"
}
```

## Configure inputs.json and runtime{}

Fovus Tokens (`benchmarkingProfileName`, `minvCpu`, `maxvCpu`, `minvCpuMemGiB`, `walltimeHours`, and the rest of the [attribute table](/docs/pipeline/miniwdl/miniwdl-config-reference.md)) are set as keys in a task's `runtime{}` block. To make a value overridable per run without editing the WDL file, declare it as a workflow input, pass it into the task call, and reference that input as the `runtime{}` value:

```wdl
version 1.0

workflow align_workflow {
    input {
        File reads
        File ref

        String benchmarkingProfileName = "Default CPU"
        Int minvCpu = 4
        Int minvCpuMemGiB = 16
    }

    call align {
        input:
            reads = reads,
            ref = ref,
            benchmarkingProfileName = benchmarkingProfileName,
            minvCpu = minvCpu,
            minvCpuMemGiB = minvCpuMemGiB,
    }

    output {
        File aligned = align.aligned
    }
}

task align {
    input {
        File reads
        File ref
        String benchmarkingProfileName
        Int minvCpu
        Int minvCpuMemGiB
    }

    command <<<
        bwa mem -t $FovusNodeVcpu ~{ref} ~{reads} > aligned.sam
    >>>

    output {
        File aligned = "aligned.sam"
    }

    runtime {
        docker: "biocontainers/bwa:latest"
        benchmarkingProfileName: benchmarkingProfileName
        minvCpu: minvCpu
        minvCpuMemGiB: minvCpuMemGiB
    }
}
```

Then override any of those values per run in `inputs.json`, without touching the WDL file:

```json
{
  "align_workflow.reads": "/fovus-storage/pipelines/genome-data/sample.fastq",
  "align_workflow.ref": "/fovus-storage/pipelines/genome-data/GRCh38.fa",

  "align_workflow.benchmarkingProfileName": "Default CPU",
  "align_workflow.minvCpu": 8,
  "align_workflow.minvCpuMemGiB": 32
}
```

Any Fovus Token you omit from `inputs.json` falls back to the WDL-declared default, or — if the WDL doesn't declare one — to your Fovus account's default job config for the chosen `benchmarkingProfileName`.

{% hint style="warning" %}
Keep these overrides at the `<workflow_name>.<input_name>` level, as shown above. `miniwdl-fovus run` also scans `inputs.json` for a separate, task-scoped key shape (`<workflow_name>.<task_name>.<attribute>`) used for pre-configuring benchmarking ahead of submission — see [Run with local miniwdl-fovus run](/docs/pipeline/miniwdl/miniwdl-submission/local-manager.md#pre-configuring-benchmarking) for that pattern and the naming collision to avoid.
{% endhint %}

For the complete Fovus Token list and their Fovus job-config field mappings, see the [miniWDL configuration reference](/docs/pipeline/miniwdl/miniwdl-config-reference.md).

## Choose how to run

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><h4><i class="fa-terminal" style="color:$primary;">:terminal:</i> Run with local miniwdl-fovus run</h4></td><td>Prerequisites, submission commands, and stop/resume behavior.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/local-manager.md">Run with local miniwdl-fovus run</a></td></tr></tbody></table>


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