Introduction

TODO

Test data

We will fetch test data from this repository: https://github.com/hartwigmedical/testdata:

git clone https://github.com/hartwigmedical/testdata testData 

Run directly from ViashHub

In order to fetch the workflow from Viash Hub, the following should be added to ~/.nextflow/scm:

providers {
  vsh {
    platform = 'gitlab'
    server = "viash-hub.com"
  }
}

Then, with the data fetched above present under testData, we can run fastqc in parallel on all 32 fastq files:

nextflow run data-intuitive/viash_hub_demo \
    -hub vsh \
    -main-script target/nextflow/workflows/parallel_qc/main.nf \
    -r main \
    --input "testData/**/*.fastq.gz" \
    --publish_dir output \
    -with-docker

The output will be stored under output as indicated by the --publish_dir argument.

Run from a local copy

First of all, build the workflow component and fetch the dependencies:

❯ viash ns build
temporaryFolder: /tmp/viash_hub_repo5484030342718552259 uri: https://github.com/openpipelines-bio/openpipeline.git
Cloning into '.'...
checkout out: List(git, checkout, tags/0.12.1, --, .) 0
Creating temporary 'target/.build.yaml' file for op as this file seems to be missing.
Exporting parallel_qc (workflows) =nextflow=> <...>/demo/target/nextflow/workflows/parallel_qc
Exporting transpose (utils) =nextflow=> <...>/demo/target/nextflow/utils/transpose
All 2 configs built successfully

Now, run fastqc on all fastq files that can be found under in the testData directory:

❯ nextflow run target/nextflow/workflows/parallel_qc/main.nf \
    --input "testData/**/*.fastq.gz"  \
    --publish_dir output \
    -with-docker