Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update README.md #4

Open
wants to merge 1 commit into
base: develop
Choose a base branch
from
Open

Update README.md #4

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
87 changes: 4 additions & 83 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,15 +1,12 @@
[![Docker Repository on Quay.io](https://quay.io/repository/collaboratory/dockstore-tool-bamstats/status "Docker Repository on Quay.io")](https://quay.io/repository/collaboratory/dockstore-tool-bamstats)
[![Build Status](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats.svg)](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats)

# 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.
A repo for the `Dockerfile` to create a Docker image for the BAMStats command.

## Validation

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

Versions that we tested with are the following
```
Expand All @@ -33,82 +30,6 @@ manually you would execute:

```
$ 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:1.25-3

# 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:1.25-3 > 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:1.25-3 --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
$ docker run -w="/home/ubuntu" -v `pwd`:/home/ubuntu --user `echo $UID`:1000 quay.io/collaboratory/dockstore-tool-bamstats:1.25-6 bamstats 4 NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
```
You'll then see a file, `bamstats_report.zip`. Using the command above, it will automatically be mounted out of the container.