action-cloudos-cli

:octocat: Github action to programmatically interact with the Lifebit CloudOS platform using the official API client cloudos-cli

action-nextflow-lint

:octocat: Nextflow linter

action-pr-lint

:octocat: PR linting for common PR issues

ampa-nf

Fast automated prediction of protein antimicrobial regions

ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

ancestryinference_king

annotate

annotatevariants

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

api-request-examples

This is a repo to host examples for deploit's api requests.

aws-s3-cp-nf

Stage files with aws s3 cp vs native Nextflow staging

bam2cram

bam2fastq

Minimal Nextflow pipeline to convert bam files into fastq files

bammetrics

A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample

bcl2fastq-nf

WORK IN PROGRESS: Nextflow pipeline to run bcl2fastq to convert BCL files to FASTQ

beagle4

beagle5

benchmarking-pipeline

bi-data-queries-resources

Notebooks and scripts for querying programmatically source and OMOP data

bin-scripts

biobank-gwas

biobank-gwas-nf

bioinfo-wrangling-scripts

bulk-sum

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

cancer-prevalence-analysis

cgpwgs-nf

Nextflow version of dockstore-cgpwgs wrapper

ching-lau-intracranial-germline-tumor

chipseq

Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.

cloudos

cloudos: An R package for the Lifebit CloudOS Platform

cloudos-cli

Python library and Command Line Interface for interacting with Lifebit Applications