dockstore-tool-bamstats

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dockstore-tool-bamstats

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A repo for the BAMStats command, used as the tutorial for Dockstore

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# dockstore-tool-bamstats

A repo for the `Dockerfile` to create a Docker image for the BAMStats command. Also contains the
`Dockstore.yml` which is used by the [Dockstore](https://www.dockstore.org) to register
this container and describe how to call BAMStats for the community.

This repo is archived in favour of https://github.com/dockstore/dockstore-tool-bamstats

## Validation

This tool has been validated as a CWL draft-3 and v1.0 CommandLineTool.

Versions that we tested with are the following 
```
avro (1.8.1)
cwl-runner (1.0)
cwl-upgrader (0.1.1)
cwltool (1.0.20190915164430)
schema-salad (4.5.20190906201758)
setuptools (25.1.6)
```

## Building Manually

Normally you would let [Quay.io](http://quay.io) build this.  But, if you need to build
manually you would execute:

docker build -t collaboratory/dockstore-tool-bamstats:1.25-7 .

## Running Manually

```
$ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam collaboratory/dockstore-tool-bamstats:1.25-7

# within the docker container
$ /usr/local/bin/bamstats 4 /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
```
You'll then see a file, `bamstats_report.zip`, in the current directory, that's the report file. You can use `-v` to mount the result out of the container.

## Running Through the Dockstore CLI

This tool can be found at the [Dockstore](https://dockstore.org), login with your GitHub account and follow the 
directions to setup the CLI.  It lets you run a Docker container with a CWL/WDL descriptor locally, using Docker and the CWL/WDL command line utility.  This is great for testing.

### With CWL

#### Make a Parameters JSON

This is the parameterization of the BAM stat tool, a copy is present in this repo called `sample_configs.json`:

```
{
  "bam_input": {
        "class": "File",
        "path": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
    },
    "bamstats_report": {
        "class": "File",
        "path": "/tmp/bamstats_report.zip"
    }
}
```

#### Run with the CLI

Run it using the `dockstore` CLI:

```
Usage:
# fetch CWL
$> dockstore tool cwl --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 > Dockstore.cwl
# make a runtime JSON template and edit it (or use the content of sample_configs.json above)
$> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 --json Dockstore.json
```

### With WDL
#### Make a Parameters JSON

This is the parameterization of the BAM stat tool, a copy is present in this repo called `test.wdl.json`:

```
{
  "bamstatsWorkflow.bam_input": "rna.SRR948778.bam",
  "bamstatsWorkflow.mem_gb": "4"
}
```

#### Run with the CLI

Run it using the `dockstore` CLI:

```
Usage:
# fetch WDL
$> dockstore tool wdl --entry quay.io/collaboratory/dockstore-tool-bamstats > Dockstore.wdl
# make a runtime JSON template and edit it (or use the content of test.wdl.json above)
$> dockstore tool convert wdl2json --wdl Dockstore.wdl > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats --json Dockstore.json
```

## Running Nextflow Workflow

Install [Nextflow](https://www.nextflow.io/). Nextflow workflows cannot be run with the Dockstore CLI yet.

The workflow can be run using the following command:
```
$> nextflow run main.nf
```

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