Rare Diseases workflow for WES-TES

This is an adaptation of Wetlab2Variations CWL workflow to make it compatible with the integrated WES-TES workflow execution environment. Most of the work was done by contributors of the upstream repository.

Requirements

To run this workflow you will need:

1. the URL of WES-TES execution environment, where the workflow will be executed
2. 5 indirect input files containing the data accessible to your workflow (e.g. present in the Local Site Storage or User Workspace of the WES-TES, where the workflow will be executed):

• 2 fastq files
• a reference genome file
• a known sites file
• a known indels file

3. 4 direct input files containing URLs of the above mentioned input files, that also need to be accessible to your workflow (e.g. uploaded to the User Workspace of the execution environment)
4. the URL of the workflow itself
5. Inputs for the workflow described as a JSON file, if you want to interact with the WES API directly, or YAML file, if you want to use WesCli command line utility.

Example

1. We will assume workflow execution environment to be installed at:

http://wes-tes-example.tsi.ebi.ac.uk

2. The datasets are present in the Local Site Storage of the environment and accesible to workflows above under URLs:

Input	URL
Fastq	http://site-storage/rd/full/U5c_CCGTCC_L001_R1_001.fastq.gz http://site-storage/rd/full/U5c_CCGTCC_L001_R2_001.fastq.gz
Reference genome	http://site-storage/rd/full/hs37d5.fa.gz
Known sites	http://site-storage/rd/full/dbsnp_138.b37.vcf.gz
Known indels	http://site-storage/rd/full/Mills_and_1000G_gold_standard.indels.b37.vcf

3. Direct input files are present in the User Workspace:

Input name	External URL	Internal URL	Contents
curl_reference_genome_url	https://wes-tes-example.tsi.ebi.ac.uk/data/tmp/rd/full/reference_seq_url.txt	file:///data/tmp/rd/full/reference_seq_url.txt	Link
curl_fastq_urls	https://wes-tes-example.tsi.ebi.ac.uk/data/tmp/rd/full/fastq_files_urls.txt	file:///data/tmp/rd/full/fastq_files_urls.txt	Link
curl_known_indels_url	https://wes-tes-example.tsi.ebi.ac.uk/data/tmp/rd/full/known_indels_url.txt	file:///data/tmp/rd/full/known_indels_url.txt	Link
curl_known_sites_url	https://wes-tes-example.tsi.ebi.ac.uk/data/tmp/rd/full/known_sites_url.txt	file:///data/tmp/rd/full/known_sites_url.txt	Link

4. The workflow URL: https://github.com/EMBL-EBI-TSI/RD_pipeline_demo/blob/master/workflow.cwl
5. Run the workflow using WesCli:

wes run rd_pipeline.yaml

from a directory that contains this file and with WesCli installed.

Or alternatively call the RunWorkflow POST API endpoint directly; you can use Swagger UI - at the example site it will be present at https://wes-tes-example.tsi.ebi.ac.uk/ga4gh/wes/v1/ui/#!/WorkflowExecutionService/RunWorkflow - to help you construct and/or execute the call. Parameters:

workflow_params : {
      "chromosome": "1",
      "curl_fastq_urls": {
        "class": "File",
        "path": "file:///data/tmp/rd/full/fastq_files_urls.txt"
      },
      "curl_known_indels_url": {
        "class": "File",
        "path": "file:///data/tmp/rd/full/known_indels_url.txt"
      },
      "curl_known_sites_url": {
        "class": "File",
        "path": "file:///data/tmp/rd/full/known_sites_url.txt"
      },
      "curl_reference_genome_url": {
        "class": "File",
        "path": "file:///data/tmp/rd/full/reference_seq_url.txt"
      },
      "lftp_out_conf": {
        "class": "File",
        "path": "http:///data/tmp/lftp.txt"
      },
      "readgroup_str": "@RG\\tID:Seq01p\\tSM:Seq01\\tPL:ILLUMINA\\tPI:330",
      "sample_name": "abc1"
    }
    workflow_type: cwl
    workflow_type_version: v1.0
    workflow_url: https://github.com/EMBL-EBI-TSI/RD_pipeline_demo/blob/master/workflow.cwl