biowdl/biowdl.github.io biowdl/biowdl.github.io

  • Stars
    star
    1
  • Language
  • Created over 6 years ago
  • Updated over 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
biowdl/biowdl.github.io
github

biowdl

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

The BioWDL organisation github.io site.

More Repositories

1

tasks

A collection of reusable WDL tasks. Category:Other
WDL
85
star
2

RNA-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
WDL
31
star
3

germline-DNA

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
WDL
23
star
4

wdl-aid

Automatic Input Documentation for WDL workflows
Python
11
star
5

wdl-packager

Package a WDL and its imports into a zip file
Python
8
star
6

structural-variantcalling

A workflow for calling structural variants. Category:Single-Sample
WDL
8
star
7

somatic-variantcalling

A pipeline for somatic variantcalling. Category:Single-Sample
WDL
8
star
8

WGSinCancerDiagnostics

WDL
7
star
9

ngs-performance-choices

Which tools to choose based on various performance metrics.
7
star
10

mkbigfifo

A script to make FIFO files (pipes) with the maximum allowed buffer size
Python
7
star
11

prepull-singularity

A tool for pulling singularity images in HPC environments.
Python
4
star
12

pipeline-template

A pipeline template for modular pipelines
WDL
3
star
13

biowdl-test-data

Reproducible and reusable test data for bioinformatics projects.
Python
3
star
14

gatk-variantcalling

A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
WDL
2
star
15

singularity-permanent-cache

Creates a permanent cache for singularity images on disk.
Python
2
star
16

QC

A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample
WDL
2
star
17

gatk-preprocess

A BioWDL workflow for preprocessing BAM files for variantcalling. Based on the GATK Best Practices. Category:Single-Sample
WDL
2
star
18

collect-columns

Python
1
star
19

scripts

Scripts for releasing, updating docs etc. in biowdl repos
Shell
1
star
20

expression-quantification

A BioWDL workflow for quantifying expression. Category:Multi-Sample
WDL
1
star
21

TALON-WDL

WDL implementation of the TALON workflow. Category:Multi-Sample InDevelopment
WDL
1
star
22

uniparental-disomy

A simple pipeline to find uniparental-disomy based on GVCF data using UPDio
1
star
23

compare-gff

A pipeline to compare a General Feature Format file to other General Feature Format files.
Scala
1
star
24

biotdg

Bioinformatics Test Data Generator
Python
1
star
25

clinical-validation

Check if a VCF for a benchmark sample matches the given output.
WDL
1
star
26

ansible-cromwell-database

Sets up a cromwell database server.
1
star
27

bam-to-gvcf

A BioWDL workflow for generating gVCF files from BAM files.
WDL
1
star
28

virus-assembly

A BioWDL pipeline for virus assembly.
WDL
1
star
29

sequence-classification

A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample
WDL
1
star