CWLs for the Argos pipeline.
The CWLs are categorized in multiple directories based on their unit of work, although the CWLs contained within can refer to other CWL directories via their relative path.
For example, each CWL module that performs at the tumor-normal pair level are contained in the modules/pair directory; workflows that perform executions by chaining multiple modules are contained in the workflows directory. The CWLs in workflows/ will reference CWLs in modules/pair/ to perform their tasks, such as alignment-pair.cwl and variant-calling.cwl.
This repo contains git submodules; make sure to git clone --recursive when downloading.
CWLs have been tested with the toil executor, found here.
Module CWLs perform small pipeline operations to do a particular task. For example, modules/pair/alignment.cwl will takes a pair of tumor-normal samples and align it with bwa mem, followed by modules/pair/realignment.cwl; this then returns a pair of tumor-normal bam files and some metrics.
Multiple CWLs in this directory will refer to other CWLs in the workflows/ and tools/ directories.
Contains CWLs for tools (bwa, bcftools, etc.) used by the modules and workflows.
Workflow CWLs that operate at either a sample level or at one paired tumor-normal level. Multiple CWLs in this directory will refer to other CWLs in the modules/ and tools/ directories.
The two CWLs listed here expect input as a list of paired tumor-normal samples.
Given a list of paired tumor-normal samples, this CWL uses workflows/pair-workflow.cwl to do alignment, variant calling, and some metrics, followed by modules/project/generate-qc.cwl to compile QC data.
Similar to project-workflow.cwl, given a list of paired tumor-normal samples, this CWL uses workflows/pair-workflow-sv.cwl to do alignment, variant calling (including structural variants), and some metrics, followed by modules/project/generate-qc.cwl to compile QC data for all tumor-normal pairs.