Dockstore

quay.io/jwerner_dkfz/pancanqc

Sat, 10 Dec 2016 12:41:38 +0000

A Docker container for PanCanQC.

quay.io/jwerner_dkfz/DKFZBiasFilter

Thu, 15 Dec 2016 15:13:27 +0000

A Docker container for the DKFZ Bias Filter.

quay.io/jhrf/telomerecat

Thu, 19 Jan 2017 12:07:33 +0000

A docker container for the telomerecat tool

quay.io/almussel/pubmunch-docker

Mon, 27 Mar 2017 13:23:37 +0000

![build_status](https://quay.io/repository/almussel/pubmunch-docker/status) A Docker container for running the Literature Searching pipeline for BRCA Exchange. Documentation for PubMunch can be found

quay.io/k-cao/dockstore-tool-bamstats

Mon, 24 Apr 2017 20:35:04 +0000

![build_status](https://quay.io/repository/collaboratory/dockstore-tool-bamstats/status) A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for m

quay.io/standage/tag-dockstore-test

Thu, 22 Jun 2017 03:25:06 +0000

A Docker container for the **tag** annotation processing library. Built for testing & exploration purposes.

quay.io/standage/megahit-dockstore

Fri, 23 Jun 2017 18:44:23 +0000

MEGAHIT assembler

registry.hub.docker.com/nathankw/dockstore-tool-bamstats

Wed, 12 Jul 2017 18:40:49 +0000

registry.hub.docker.com/mazumderlab/biomuta_docker_image

Mon, 12 Mar 2018 18:31:07 +0000

A Docker container for the BioMuta Database. See the https://hive.biochemistry.gwu.edu/biomuta website for more information.

registry.hub.docker.com/opengenomics/muse

Tue, 13 Mar 2018 20:03:51 +0000

registry.hub.docker.com/opengenomics/mutect

Tue, 13 Mar 2018 20:08:31 +0000

registry.hub.docker.com/opengenomics/fpfilter

Tue, 13 Mar 2018 20:13:19 +0000

registry.hub.docker.com/opengenomics/radia

Tue, 13 Mar 2018 20:24:53 +0000

Runs radia on individual chromosomes, then merges output. An input DNA (exome) sample pair is required, additional RNA-Seq data for the same sample is advised but optional. Radia performes significant

registry.hub.docker.com/opengenomics/radia

Tue, 13 Mar 2018 20:26:23 +0000

Filter radia output. If the input is from exomes plus RNA-Seq, set dnaOnly to False

registry.hub.docker.com/opengenomics/somatic-sniper

Tue, 13 Mar 2018 20:32:43 +0000

registry.hub.docker.com/opengenomics/varscan

Tue, 13 Mar 2018 20:35:17 +0000

quay.io/briandoconnor/dockstore-workflow-md5sum-tester

Fri, 16 Mar 2018 18:17:22 +0000

[![Docker Repository on Quay.io](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum/status "Docker Repository on Quay.io")](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum)

registry.hub.docker.com/broadinstitute/pcawg_broad_wgs_variant_callers

Wed, 11 Apr 2018 21:14:29 +0000

registry.hub.docker.com/sevenbridges/pcawg_muse_sbg_modified

Wed, 23 May 2018 12:30:22 +0000

registry.hub.docker.com/sevenbridges/pcawg_sanger_sbg_modified

Wed, 23 May 2018 12:31:14 +0000

registry.hub.docker.com/sevenbridges/pcawg_delly_sbg_modified

Thu, 24 May 2018 09:56:01 +0000

registry.hub.docker.com/sevenbridges/pcawg_dkfz_sbg_modified

Thu, 24 May 2018 13:23:12 +0000

quay.io/anmoljh/docker-delly

Mon, 09 Jul 2018 14:12:05 +0000

A Docker container for SV analysis using Delly tool.

quay.io/mduran/generate-igv-session_2

Tue, 17 Jul 2018 15:39:31 +0000

github.com/nf-core/eager

Wed, 12 Sep 2018 19:38:50 +0000

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

quay.io/ga4gh-dream/dockstore-tool-synapse-submit

Thu, 13 Sep 2018 16:01:06 +0000

[![Docker Repository on Quay.io](https://quay.io/repository/ga4gh-dream/dockstore-tool-synapse-submit "Docker Repository on Quay.io")](https://quay.io/thomasyu888/dockstore-tool-synapse-submit) The Sy

quay.io/ga4gh-dream/dockstore-tool-helloworld-checker

Thu, 13 Sep 2018 16:01:06 +0000

registry.hub.docker.com/lynnlangit/blastn-jupyter-docker

Fri, 15 Feb 2019 04:10:59 +0000

quay.io/collaboratory/dockstore-tool-bamstats

Wed, 29 May 2019 02:58:00 +0000

registry.hub.docker.com/jamesrcounts/variantspark

Wed, 29 May 2019 19:16:34 +0000

This is a docker container which runs the default command using a container with VariantSpark.

registry.hub.docker.com/lynnlangit/blastn

Sat, 01 Jun 2019 22:33:44 +0000

registry.hub.docker.com/lynnlangit/blastn

Sun, 02 Jun 2019 17:08:43 +0000

quay.io/jmonlong/dockstore-ktag

Tue, 17 Sep 2019 19:50:48 +0000

![build_status](https://quay.io/repository/jmonlong/dockstore-ktag/status) A Docker container for the Ktag command.

registry.hub.docker.com/mruffalo/star-grch38

Tue, 15 Oct 2019 13:08:04 +0000

STAR aligner, 2.6.1e with GRCh38 index

quay.io/pancancer/pcawg-muse

Wed, 16 Oct 2019 01:22:09 +0000

PCAWG MuSE variant calling workflow is developed by MD Anderson Cancer Center (http://bioinformatics.mdanderson.org/main/MuSE), it consists of software component calling structural variants using unif

quay.io/f73chen/dockstore-tool-bamstats

Tue, 26 May 2020 21:42:24 +0000

[![Docker Repository on Quay.io](https://quay.io/repository/collaboratory/dockstore-tool-bamstats/status "Docker Repository on Quay.io")](https://quay.io/repository/collaboratory/dockstore-tool-bamsta

registry.hub.docker.com/g3chen/new_account_bamstats

Thu, 28 May 2020 19:21:59 +0000

quay.io/f73chen/dockstore-test3

Thu, 11 Jun 2020 14:31:02 +0000

# DockstoreToolPractice Practicing making and publishing a Dockstore tool

registry.hub.docker.com/g3chen/output-test

Thu, 11 Jun 2020 14:31:32 +0000

# DockstoreToolPractice Practicing making and publishing a Dockstore tool

registry.hub.docker.com/karchinlab/opencravat-cwl-install

Wed, 22 Jul 2020 19:42:41 +0000

# OpenCRAVAT CWL Tool This container and cwl wrapper define a way to run OpenCRAVAT within CWL on platforms such as DNANexus and SevenBridges. Modules are tarred and gzipped and passed as inputs to t

registry.hub.docker.com/karchinlab/opencravat

Wed, 22 Jul 2020 19:53:45 +0000

# OpenCRAVAT CWL Tool This container and cwl wrapper define a way to run OpenCRAVAT within CWL on platforms such as DNANexus and SevenBridges. Modules are tarred and gzipped and passed as inputs to t

quay.io/ibrahimjabarkhel/toolkit-for-generating-test-data

Tue, 04 Aug 2020 22:24:57 +0000

This toolkit was developed with the goal of creating genomic test data by subsetting and downsampling BAM, CRAM, and SAM files. As a developer, we use test data often. It's sometimes better to use a s

github.com/broadinstitute/warp/IlluminaGenotypingArray

Fri, 07 Aug 2020 18:13:07 +0000

# Welcome to WARP WARP (WDL Analysis Research Pipelines) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform and coll

registry.hub.docker.com/weischenfeldt/pcawg_delly_workflow

Tue, 25 Aug 2020 12:01:45 +0000

![pcawg logo](https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/pcawg_delly_workflow/2.0.0/img/PCAWG-final-small.png "pcawg logo") **PCAWG DELLY Workflow** The DELLY workflow from the ICGC PanCa

registry.hub.docker.com/weischenfeldt/bric-embl_delly_workflow

Tue, 25 Aug 2020 12:01:45 +0000

![build_status](https://img.shields.io/docker/build/weischenfeldt/bric-embl_delly_workflow.svg) ![docker_pulls](https://img.shields.io/docker/pulls/weischenfeldt/bric-embl_delly_workflow.svg) ![docker

registry.hub.docker.com/weischenfeldt/svaba_workflow

Tue, 25 Aug 2020 12:01:45 +0000

registry.hub.docker.com/weischenfeldt/pcawg_sv_merge

Tue, 25 Aug 2020 12:01:45 +0000

![build_status](https://img.shields.io/docker/build/weischenfeldt/pcawg_sv_merge.svg) A Docker container for the pcawg_sv_merge_workflow.

registry.hub.docker.com/weischenfeldt/csvc

Tue, 25 Aug 2020 13:44:32 +0000

![build_status](https://img.shields.io/docker/build/weischenfeldt/csvc.svg) ![docker_pulls](https://img.shields.io/docker/pulls/weischenfeldt/csvc.svg) ![docker_builds](https://img.shields.io/docker/a

github.com/broadinstitute/warp/JointGenotyping

Thu, 01 Oct 2020 19:31:30 +0000

github.com/broadinstitute/warp/ExomeGermlineSingleSample

Thu, 01 Oct 2020 19:31:31 +0000

### WDL Analysis Research Pipelines The WDL Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data Sc

registry.hub.docker.com/sevenbridges/pcawg_bwa_sbg_modified

Tue, 20 Oct 2020 12:10:50 +0000

The BWA-Mem workflow from the ICGC PanCancer Analysis of Whole Genomes (PCAWG) project. For more information see the PCAWG project [page](https://dcc.icgc.org/pcawg) and the GitHub [page](https://gith

quay.io/jlanej/mosdepth-docker

Thu, 02 Sep 2021 21:27:12 +0000

github.com/broadinstitute/warp/Imputation

Mon, 20 Sep 2021 18:12:24 +0000

### Warp Analysis Research Pipelines The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data

github.com/broadinstitute/warp/CramToUnmappedBams

Thu, 27 Jan 2022 01:24:12 +0000

### Warp Analysis Research Pipelines The Warp Analysis Research Pipelines (WARP) repository is a collection of cloud-optimized pipelines for processing biological data from the Broad Institute Data

github.com/dockstore/dockstore-tool-bamstats/bamstats_cwl

Thu, 11 Aug 2022 17:23:49 +0000

github.com/dockstore/dockstore-tool-bamstats/bamstats_sort_cwl

Thu, 11 Aug 2022 17:23:49 +0000

This demonstrates an alternate descriptor to Dockstore.cwl A Docker container for the sort command using a container shared with bamstats.

github.com/common-workflow-library/bio-cwl-tools/picard_CreateSequenceDictionary

Wed, 17 Aug 2022 17:29:37 +0000

Create a SAM/BAM file from a fasta containing reference sequence. The output SAM file contains a header but no SAMRecords, and the header contains only sequence records.

github.com/common-workflow-library/bio-cwl-tools/picard_MarkDuplicates

Wed, 17 Aug 2022 17:29:37 +0000

Removal of duplicates from aligned reads.

github.com/common-workflow-library/bio-cwl-tools/picard_SortSam

Wed, 17 Aug 2022 17:29:38 +0000

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