kopalgarg24 / wdlmerge

merge multiple WDLs

WDLMerge

Merge WDLs

Installation

Install WDLMerge with pip

  pip install -i https://test.pypi.org/simple/ WDLMerge==0.1.1
  pip install miniwdl

Requirements

• miniwdl

To run in Google Colab

from WDLMerge import *
import WDL
import asyncio
import nest_asyncio
import WDL

# Allow nested event loops in Jupyter notebook
nest_asyncio.apply()

Examples

Merge WDLs

wdl=merge_wdls(WDLs=["WDL_1.wdl", "WDL_2.wdl"])

Merge WDLs and Specify Task Order in Workflow

merged_wdl = merge_wdls(WDLs=["WDL_1.wdl", "WDL_2.wdl"], tasks_order=['task1', 'task3', 'task2'])

Validate WDL

validate_wdl('WDL_1.wdl')

Upgrade WDL

# Get a WDL written in one of the older versions
!wget https://raw.githubusercontent.com/gatk-workflows/gatk4-germline-snps-indels/1.1.2/joint-discovery-gatk4-local.wdl
upgrade_wdl('joint-discovery-gatk4-local.wdl')

TODO

• specify WDL task order

Notes to self

• To update the package do the following:

# update version in toml
python3 -m build
# delete the previous tar
python3 -m twine upload --repository testpypi dist/*