robsyme
Open data, open science, open and decentralised publishing. Data wrangling, molecular biology, genomics and bioinformatics. Research scientist. Novice human.
Seqera LabsMontréal, QC, Canada
Pinned Repositories
bioruby-chado
A library that allows you to pull ruby objects out of a Chado-schema database
cegma-docker
Docker container for running CEGMA
docker-REPET
The REPET package in a container.
docker-sge
Dockerfile to build a container with SGE installed
gortex
Tool to pull out species-specific sequence from coloured graphs generated by Cortex-var
nextflow-annotate
Workflows I find helpful for fungal genome annotation
nf-annotate
Fungal genome annotation pipeline
nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
obo
A parser for the OBO flat file format
succinctBitSet
Fast rank and select operations on indexed bitsets.
robsyme's Repositories
robsyme/modules
Minimal nf-core style modules repository
robsyme/20231211_ticket_4242
robsyme/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
robsyme/branch-testing
robsyme/fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
robsyme/funcscan
(Meta-)genome screening for functional and natural product gene sequences
robsyme/java-ipld-cbor
A Java implementation of the IPLD cbor format
robsyme/manta-testing
robsyme/minimal
robsyme/multi-package-containers
Testing building mulled containers for multi-requirement tools.
robsyme/mythical.fish
My portfolio, built using Gatsby, PostCSS, Tailwind, and PurgeCSS. 🐠
robsyme/nextflow
A DSL for data-driven computational pipelines
robsyme/nextflow-example
robsyme/nf-aggregate
Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform (beta)
robsyme/nf-hello
Nextflow plugin implementation skeleton
robsyme/nf-quilt
robsyme/nf-test
A repository for various tests and minimal-reproducible-example workflows
robsyme/nf-weblog
Implement weblog plugin for Nextflow
robsyme/nonroot-main-nf
robsyme/quiltcore-java
Java implementation of the Quilt API
robsyme/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
robsyme/showcase
Infrastructure as code implementation of the seqeralabs/showcase Workspace in Tower Cloud
robsyme/slas-demo
Demonstration repository for SLAS 2024
robsyme/smrnaseq
A small-RNA sequencing analysis pipeline
robsyme/test-branching
Test repo for debugging Tower behaviour
robsyme/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
robsyme/tower-cli
Nextflow Tower CLI tool
robsyme/waitlift
A small application for stress testing the filesystem
robsyme/wf-clone-validation
robsyme/xenome
Dummy repo for stress testing fusion with xenome