A repo for the dockstore.yml
which is used by the Dockstore to register
this tool/workflow and describe how to call edge-covid19 for the community.
$ git clone https://github.com/chienchi/dockstore-edge-covid19.git
$ cd dockstore-edge-covid19
$ docker run -it --rm -v `pwd`:/repo bioedge/edge-covid19 bash
# within the docker container
perl /home/edge/edge/runPipeline -c /repo/configs/config.illumina.txt -o /repo/testing -cpu 3 -noColorLog -p /repo/test/SARS-COVID-test-swift-v2.1.fastq /repo/test/SARS-COVID-test-swift-v2.2.fastq
You'll then see a output directory, /repo/testing
, that's the project output files. You can also see the testing
result directory out of the container. A report HTML file testing/HTML_Report/report.html
can be opened and visualized in host environment.
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.
This is the parameterization of the edge-covid19 workflow, a copy is present in this repo called test/test.wdl.json
:
{
"edgecovid19Workflow.EDGEconfig": "configs/config.illumina.trim_swift_primer.txt",
"edgecovid19Workflow.projName":"edgecovid19_test",
"edgecovid19Workflow.Read_1":"test/SARS-COVID-test-swift-v2.1.fastq",
"edgecovid19Workflow.Read_2":"test/SARS-COVID-test-swift-v2.2.fastq",
"edgecovid19Workflow.mem_gb": 8,
"edgecovid19Workflow.cpu": 3
}
There are several pre-configured config files in the configs
sub-directory. If you are familier with EDGE configuration file, you can edit the file correspondingly for your sample.
- config.ONT.txt: default EDGE configuration file for Nanopore reads
- config.ONT.trim_artic_primer_v1.txt: EDGE configuration file for Nanopore reads with artic primer v1 trimming.
- config.ONT.trim_artic_primer_v2.txt: EDGE configuration file for Nanopore reads with artic primer v2 trimming.
- config.ONT.trim_artic_primer_v3.txt: EDGE configuration file for Nanopore reads with artic primer v3 trimming.
- config.ONT.trim_artic_primer_v4.txt: EDGE configuration file for Nanopore reads with artic primer v4 trimming.
- config.ONT.trim_cdc_primer.txt: EDGE configuration file for Nanopore reads with CDC primer SC2_200324 trimming.
- config.ONT.trim_swift_primer.txt: EDGE configuration file for Nanopore reads with SWIFT primer v2 trimming.
- config.illumina.txt: default EDGE configuration file for Illumina reads
- config.illumina.trim_artic_primer_v1.txt: EDGE configuration file for Illumina reads with artic primer v1 trimming.
- config.illumina.trim_artic_primer_v2.txt: EDGE configuration file for Illumina reads with artic primer v2 trimming.
- config.illumina.trim_artic_primer_v3.txt: EDGE configuration file for Illumina reads with artic primer v3 trimming.
- config.illumina.trim_artic_primer_v4.txt: EDGE configuration file for Illumina reads with artic primer v4 trimming.
- config.illumina.trim_cdc_primer.txt: EDGE configuration file for Illumina reads with CDC primer SC2_200324 trimming.
- config.illumina.trim_swift_primer.txt: EDGE configuration file for Illumina reads with SWIFT primer v2 trimming.
Run it using the dockstore
CLI:
Usage:
# make a runtime JSON template and edit it (or use the content of test.wdl.json above)
$> dockstore tool convert entry2json --descriptor wdl --entry quay.io/chienchi/dockstore-edge-covid19:latest > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore tool launch --entry quay.io/chienchi/dockstore-edge-covid19:latest --json Dockstore.json --descriptor wdl
maintainer: Chienchi Lo [email protected]