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.

Validation

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

Versions that we tested with are documented iin https://raw.githubusercontent.com/dockstore/dockstore/1.13.0-beta.3/dockstore-webservice/src/main/resources/requirements/1.13.0/requirements3.txt

Building Manually

Normally you would let GitHub actions build this. But, if you need to build manually (for example due to broadinstitute/cromwell#6827) you would execute:

docker build -t ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8 .

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 ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8

# 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:

# Fetch CWL workflow
dockstore workflow cwl --entry github.com/dockstore/dockstore-tool-bamstats/bamstats_cwl:develop > bamstats.cwl

# Make a runtime JSON template and edit it (or use the content of sample_configs.json above)
dockstore workflow convert cwl2json --cwl bamstats.cwl > Dockstore.json

# Update the "path" field for both input and output files within Dockstore.json
jq '.bam_input.path |= "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"| .bamstats_report.path |= "/tmp/bamstats_report.zip"' Dockstore.json | sponge  Dockstore.json

# Run it locally with the Dockstore CLI
dockstore workflow launch --entry github.com/dockstore/dockstore-tool-bamstats/bamstats_cwl:develop --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 workflow wdl --entry github.com/dockstore/dockstore-tool-bamstats/wdl:develop > bamstats.wdl
# make a runtime JSON template and edit it (or use the content of test.wdl.json above)
$> dockstore workflow convert wdl2json --wdl bamstats.wdl > Dockstore.json
# the WDL cromwell engine powers the Dockstore CLI but can be chatty, to reduce distracting warnings you can do the following
$> printf "cromwell-vm-options: -DLOG_LEVEL=ERROR" >> ~/.dockstore/config
# then run it locally with the Dockstore CLI
$> dockstore workflow launch --entry github.com/dockstore/dockstore-tool-bamstats/wdl:develop --json test.wdl.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