> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/bam-collapsing/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/bam-collapsing/quickstart.md).

# Quickstart

## Step 1: Clone the workflow

```
$ git clone --recursive https://github.com/msk-access/bam_collapsing.git
$ cd bam_collapsing
$ git submodule init
```

## Step 2: Install Toil and cwltool

```
$ pip install toil[cwl]==4.2.0
```

Note: you may use any CWL executor available, provided it works with your batch system

## Step 3: Create an inputs file

As specified in:

{% content-ref url="/pages/-LsY8gHMFT22Cx6j7v81" %}
[Inputs Description](/bam-collapsing/inputs-description.md)
{% endcontent-ref %}

### Step 4 - Run the workflow with a CWL executor:

```
$ cwltool bam_collapsing.cwl inputs.json
```

Or, to run the workflow on a HPC cluster using toil:

```
$ toil-cwl-runner \
    --singularity \
    --jobStore my_jobStore \
    --batchSystem lsf \
    --workDir `pwd` \
    --outdir `pwd` \
    --logFile cwltoil.log \
    --writeLogs `pwd` \
    --logLevel DEBUG \
    --retryCount 2 \
    --disableCaching \
    --maxLogFileSize 20000000000 \
    --stats \
    bam_collapsing.cwl \
    inputs.yaml
```

{% hint style="info" %}
**Note:** To see help for the inputs for any cwl workflow you can use:

$ cwltool bam\_collapsing.cwl --help
{% endhint %}