BioWDL

Bioinformatics workflows and tasks, written in WDL.

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taskstasksPublic
A collection of reusable WDL tasks. Category:Other
WDL 86 30
RNA-seqRNA-seqPublic
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
WDL 31 18
germline-DNAgermline-DNAPublic
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
WDL 26 7
wdl-packagerwdl-packagerPublic
Package a WDL and its imports into a zip file
Python 7 2
wdl-aidwdl-aidPublic
Automatic Input Documentation for WDL workflows
Python 12 3
ngs-performance-choicesngs-performance-choicesPublic
Which tools to choose based on various performance metrics.
8

Repositories

Showing 10 of 73 repositories

long-read-variant-calling Public
Long read variant calling pipeline
biowdl/long-read-variant-calling’s past year of commit activity
WDL0MIT0 0 0 UpdatedMar 28, 2025
tasks Public
A collection of reusable WDL tasks. Category:Other
biowdl/tasks’s past year of commit activity
WDL 86MIT 30 1 1 UpdatedMar 28, 2025
clinical-validation Public
Check if a VCF for a benchmark sample matches the given output.
biowdl/clinical-validation’s past year of commit activity
WDL 1MIT0 0 1 UpdatedMar 12, 2025
wdl-aid Public
Automatic Input Documentation for WDL workflows
biowdl/wdl-aid’s past year of commit activity
Python 12MIT 3 1 0 UpdatedSep 5, 2024
WGSinCancerDiagnostics Public
biowdl/WGSinCancerDiagnostics’s past year of commit activity
WDL 7MIT0 0 0 UpdatedJun 6, 2024
nanopore-sv Public
A pipeline for Oxford nanopore ont structural variant calling
biowdl/nanopore-sv’s past year of commit activity
0MIT0 0 0 UpdatedFeb 13, 2024
germline-DNA Public
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
biowdl/germline-DNA’s past year of commit activity
WDL 26MIT 7 1 1 UpdatedMay 4, 2023
structural-variantcalling Public
A workflow for calling structural variants. Category:Single-Sample
biowdl/structural-variantcalling’s past year of commit activity
WDL 8MIT 3 0 0 UpdatedMay 2, 2023
gatk-variantcalling Public
A pipeline that calls variants on a group of BAM files. Category:Multi-Sample
biowdl/gatk-variantcalling’s past year of commit activity
WDL 2MIT 3 0 0 UpdatedMay 2, 2023
QC Public
A BioWDL workflow for gathering QC metrics on and prepocessing FASTQ files. Category:Single-Sample
biowdl/QC’s past year of commit activity
WDL 2MIT 2 2 0 UpdatedMay 1, 2023