Pinned Repositories
pluto-cwl
CWL workflows for helix filter scripts
IR-interpreter
Web app for clinical interpretation of Ion Reporter variant results
NGS580-nf
Target exome sequencing analysis for NYU NGS580 gene panel
Bioinformatics
Bioinformatics analysis scripts, workflows, general code examples
IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
image-sort
Program to sort images by average color values
nextflow-demos
Example Nextflow pipelines and programming techniques
reference-annotations
Makefile for reference annotations for genes & genomic regions
reportIT
IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
stevekm's Repositories
stevekm/IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
stevekm/nextflow-demos
Example Nextflow pipelines and programming techniques
stevekm/reference-annotations
Makefile for reference annotations for genes & genomic regions
stevekm/dotfiles
Custom .bashrc, custom logger script
stevekm/toolbox
handy scripts & notes for reference
stevekm/duh
human readable disk usage reporting
stevekm/fastq-split
program for splitting a fastq file into separate files
stevekm/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
stevekm/transcript-converter-go
stevekm/nf-niceutils
nice utility methods for Nextflow pipelines
stevekm/pg-elk
Example Postgres database connection to Kibana via ElasticSearch and Logstash
stevekm/bobs-pipeline
Bob's Burgers Hamburger Making Nextflow Pipeline
stevekm/dupefinder
program to find duplicate files
stevekm/go-env
Quick setup for a conda based Golang development environment
stevekm/hashsnail
program to crack hash values
stevekm/helix_filters_01
Workflows for post-pipeline data processing and file generation
stevekm/mysql-elk
demo of using MySQL + Logstash and ELK
stevekm/nextflow-plugins-registry
Nextflow plugins index repository
stevekm/nf-hello
Nextflow plugin implementation skeleton
stevekm/nf-plugin-template
An unofficial template to build Nextflow Plugins
stevekm/nf-prov
stevekm/nf-test
Simple test framework for Nextflow pipelines
stevekm/pluto
Utilities for pluto-cwl and helix_filters repos
stevekm/pluto-cwl
CWL workflows for helix filter scripts
stevekm/pytest-workflow
Configure workflow/pipeline tests using yaml files.
stevekm/renv-Docker-conda
demo of usage of R renv with Docker and conda / mamba
stevekm/squish
fastq file compression program
stevekm/test-nf-plugin1
stevekm/transcript-converter
stevekm/unittest-parallel-demo
how to run Python unittest test cases in parallel