Workflow Tool Python Packages

highway

Python SDK for Highway Workflow Engine

picard-metrics-sqlite

store picard metrics in sqlite

bam-readgroup-to-json

Extract a readgroup from a BAM, and write it as json

merge-sqlite

merge arbitrary number of sqlite files

readgroup-json-db

read readgroup data as json and store in sqlitedb

fastqc-db

store FastQC data/summary in sqlitedb

taskcontrol

Control, Create, Run named workflows & tasks with before/after middlewares support, data persistence, orm, authentication, logging, multi-threading/processing, events, network sockets, webhooks, client-agent libraries, etc with plugins support [Actively Developed, Funding Invited] - pip3 install taskcontrol https://pypi.org/project/taskcontrol

fastqc-sqlite

store FastQC data/summary in sqlitedb

samtools-metrics-sqlite

store samtools metrics in sqlite

fastqc-to-json

fastqc to json for bwa cwl