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Java |
4 |
Some commonly used JAVA tools |
Dec 28, 2022 |
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None |
9 |
Quick lookup documents for commonly used tools |
May 23, 2022 |
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Dockerfile |
8 |
Dockerfiles for tools commonly used for phylogenetic analyses |
Mar 06, 2023 |
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wdl |
4 |
Workflows for somatic short variant discovery with GATK4 |
Jul 19, 2022 |
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wdl |
4 |
Repo For the WDL Testathon held February 18 - 19, 2020 |
Mar 20, 2020 |
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wdl |
4 |
ENCODE DNase-seq pipeline |
Feb 28, 2021 |
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wdl |
6 |
A coot trans flag using GitHub language colors! |
Apr 19, 2022 |
pb-human-wgs-workflow-wdl
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wdl |
6 |
None |
Jul 25, 2022 |
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wdl |
7 |
bioinformatics pipelines |
Mar 10, 2022 |
|
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wdl |
7 |
This is primarily a repo for capturing policies and discussions around the different workflows for … |
Jan 31, 2022 |
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wdl |
8 |
None |
Jul 14, 2022 |
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wdl |
10 |
Utility workflows for the DSP hydro.gen team (formerly palantir) |
Apr 03, 2022 |
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wdl |
10 |
a place for topmed workflows |
Feb 03, 2022 |
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wdl |
12 |
None |
May 27, 2022 |
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wdl |
2 |
A Dockstore WDL Workflow that uses UShER to place your consensus.fasta sequences on the SARS-CoV-2 … |
Nov 13, 2021 |
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wdl |
2 |
WDL workflows to build genetic maps from sequencing reads |
Mar 16, 2023 |
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wdl |
2 |
Metagenome Annotation Workflow |
Apr 25, 2023 |
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wdl |
2 |
None |
Apr 25, 2023 |
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wdl |
13 |
Evaluating genome assemblies |
Apr 18, 2023 |
public_health_bacterial_genomics
|
wdl |
24 |
None |
Mar 14, 2023 |
public_health_bioinformatics
|
wdl |
6 |
None |
Apr 17, 2023 |
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|
wdl |
30 |
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, … |
Dec 14, 2022 |
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wdl |
4 |
None |
Mar 07, 2023 |
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wdl |
38 |
Cloud-based scalable and efficient single-cell genomics workflows |
Dec 14, 2022 |
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wdl |
2 |
A Cromwell workflow to call and filter variants from sequencing data. |
Mar 28, 2022 |
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wdl |
5 |
Abraham's lab - ChipSeq Pipeline |
Feb 24, 2023 |
cromwell-output-reorganization
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wdl |
2 |
None |
Apr 26, 2022 |
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|
wdl |
2 |
Workflows used for germline short variant discovery in WGS data - replaced by https://github.com/microsoft/gatk4-genome-processing-pipeline-azure |
Jul 19, 2022 |
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wdl |
2 |
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools |
Jul 19, 2022 |
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wdl |
2 |
Workflows for converting between sequence data formats |
Jul 19, 2022 |
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wdl |
2 |
Subroutines of WARP for germline exome calling |
Jul 20, 2022 |
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wdl |
2 |
Cromwell integration testing environment |
Dec 11, 2020 |
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wdl |
2 |
Autogenerated WDLs for GATK Tools |
Jan 05, 2022 |
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wdl |
2 |
Sample dockstore whalesay repo for testing |
Nov 22, 2021 |
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wdl |
2 |
Pipeline Workflows |
Oct 20, 2019 |
topmed-workflow-variant-calling
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wdl |
2 |
None |
Jun 20, 2020 |
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wdl |
3 |
Workflows used for processing whole genome sequence data + germline variant calling. |
Jul 19, 2022 |
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wdl |
3 |
Workflows to run ADAPT on AWS Batch. |
Mar 03, 2022 |
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wdl |
3 |
Broad fungal method repository |
Mar 22, 2022 |
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wdl |
3 |
Cromwell template for running on UGER with Singularity |
Jul 19, 2021 |
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wdl |
3 |
Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for … |
Jun 28, 2022 |
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wdl |
3 |
Workflow for metagenome assembly |
Oct 28, 2021 |
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wdl |
3 |
Metatranscriptomics workflow |
May 03, 2022 |
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wdl |
20 |
HiC uniform processing pipeline |
Aug 21, 2022 |
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wdl |
26 |
ENCODE long read RNA-seq pipeline |
Aug 09, 2022 |
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wdl |
32 |
simple comparison of snakemake, nextflow and cromwell/wdl |
Jul 21, 2022 |
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wdl |
41 |
viral-ngs: complete pipelines |
Jul 11, 2022 |
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|
wdl |
52 |
Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline |
Dec 03, 2021 |
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wdl |
69 |
Educational materials for learning WDL |
Jul 19, 2022 |
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wdl |
90 |
A structural variation pipeline for short-read sequencing |
Jul 25, 2022 |