dockstore-edge-covid19

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.

Running Manually

$ 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.

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 WDL

Make a Parameters JSON

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 with the CLI

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

Point of contact

maintainer: Chienchi Lo [email protected]

hawthornprince / dockstore-edge-covid19 Goto Github PK