Pinned Repositories
actions-runners
Instructions and scripts for custom GitHub Actions runners
class-modules
A subset of curated nf-core/module and module templates
Draw-centromere-with-karyoploteR
Drawing centromere constriction at chromosome ideograms, plotted with karyoploteR package from R
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nextflow-website
Nextflow public web site
tools
Python package with helper tools for the nf-core community.
nf-co2footprint
[WIP] A Nextflow plugin to estimate the CO2 footprint of pipeline runs.
nf-validation
Params validation plugin for Nextflow pipelines
crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
tools
Python package with helper tools for the nf-core community.
mirpedrol's Repositories
mirpedrol/class-modules
A subset of curated nf-core/module and module templates
mirpedrol/Draw-centromere-with-karyoploteR
Drawing centromere constriction at chromosome ideograms, plotted with karyoploteR package from R
mirpedrol/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
mirpedrol/nextflow-website
Nextflow public web site
mirpedrol/tools
Python package with helper tools for the nf-core community.
mirpedrol/actions-runners
Instructions and scripts for custom GitHub Actions runners
mirpedrol/aws_igenomes
configuration for an iGenomes refgenieserver
mirpedrol/bioconda-recipes
Conda recipes for the bioconda channel.
mirpedrol/configs
Config files used to define parameters specific to compute environments at different Institutions
mirpedrol/containers
Bioinformatics containers
mirpedrol/crisprseq
[Under construction] A pipeline for all crispr analyses
mirpedrol/funcscan
(Meta-)genome screening for functional and natural product gene sequences
mirpedrol/mirpedrol
mirpedrol/multi-package-containers
Testing building mulled containers for multi-requirement tools.
mirpedrol/multiplesequencealign
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
mirpedrol/nextflow
A DSL for data-driven computational pipelines
mirpedrol/nf-class
Wrapper around nf-core/tools to work with class-modules
mirpedrol/nf-co2footprint
mirpedrol/nf-schema
Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
mirpedrol/paths-filter
Conditionally run actions based on files modified by PR, feature branch or pushed commits
mirpedrol/plugins
Nextflow plugins index repository
mirpedrol/recipes
recipes & asset classes definitions
mirpedrol/refgenconf
A Python object for standardized reference genome assets.
mirpedrol/refgenie
Reference genome resource manager
mirpedrol/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
mirpedrol/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
mirpedrol/setup_mac
Instructions and scripts to set up my new MAC
mirpedrol/test-datasets
Test data to be used for automated testing with the nf-core pipelines
mirpedrol/testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.
mirpedrol/website
Code and files for the main nf-core website.