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 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 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, 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. Nextflow workflows cannot be run with the Dockstore CLI yet.

The workflow can be run using the following command:

$> nextflow run main.nf