moka-guys Goto Github PK

multiqc_plugins

MultiQC modules for custom software and pipeline QC metrics at the SEGLH

ngrok_start

Allow SSH access to the system by running ngrok as a background process

ngs

ngtransition

Scripts associated with converting pipeline over from using NextGene utilities

oncodeep_upload

overlapping_genes

panelapp_api

Accesses the panelapp API and returns two files containing a list of gene symbols and ensembl ids for each gene panel

penetrance

polyedge

Finds variants at the edge of a poly that is is varying length

process_duty_csv

This repository contains the script for processing Duty CSVs on Trust Windows PC

project_requirements

Project requirement document templates

qiagen_upload

rpkm

SUPERSEDED BY EXOME DEPTH. Tools used to generate RPKM data from BAM files. Makes use of Conifer CF_bam2RPKM function to generate RPKM. Contains a wrapper script called rpkmanalysis.py which processes a list of BAMs and outputs RPKM text files to a specific output folder.

samplesheet_validator

A package to validate the formatting of Illumina SampleSheets and which notifies the user of any issues

seglh-cnv

Scripts and docker images to run CNV pipelines

seglh-naming

SEGLH naming schemes

seglh-toolbox

Source code for third party tools that have been verified/validated for use, as docker images

snp_array_transition_211220

Various scripts for use with the array software

snp_genotyping

OBSOLETE - unlikely to have any benefit over using hap.py. In-house sample matching service - may become useful if we stop sanger confirming and use SNPS instead for sample ID

snp_haplotyper

BASHer (BiAllellic SNP Haplotyper). This script filters and classifies SNPs for SNP Array data

soteria

Samplesheet uploader and validator

ssh_n_move

ssh_to_genapp

OBSOLETE: Was used for 100KGP related tasks. ssh_n_run.py is called by Moka from a trust machine to execute a command on the genapp server

summarise_gene_panel

OBSOLETE: One-off research project, summarising coverage of a set of genes

swift56_cosmic_known_variants

OBSOLETE: One-off usage. Used during SWIFT57G assay validation

swift_amplicon_annotations

OBSOLETE: One-off usage. Used during SWIFT57G assay validation

swift_scripts

Scripts used to set off amplivar

trend_analysis

A script to create per test type and per sequencer trend analysis reports using MultiQC output files.

undocking

Tools to backup and move images from dockerhub

validation

Scripts and workflows to perform NGS validations