Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/long-read-pipelines

Long read production pipelines

https://github.com/broadinstitute/long-read-pipelines

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    8 of 13 committers (61.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.8%) to scientific vocabulary

Keywords

de-novo-assembly long-reads pipelines variant-calling wdl

Keywords from Contributors

genome bioinformatics cromwell dna gatk ngs sequencing
Last synced: 6 months ago · JSON representation

Repository

Long read production pipelines

Basic Info
Statistics
  • Stars: 147
  • Watchers: 15
  • Forks: 25
  • Open Issues: 121
  • Releases: 151
Topics
de-novo-assembly long-reads pipelines variant-calling wdl
Created almost 7 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

Generic badge CI/CD Nightly

Long read pipelines

This repository contains pipelines for processing of long read data from PacBio and/or Oxford Nanopore platforms. The pipelines are written in WDL 1.0 intended for use with Google Cloud Platform via the scientific workflow engine, Cromwell. Processing is designed to be reasonably consistent between both long read platforms, and use platform-specific options or tasks where necessary.

High level workflows can be found in the wdl/ directory.

Documentation: Documentation for each workflow can be found at the repository site.

External Contributors: Please see the Contributing Guidelines for information on how to contribute to the repository.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Release event: 25
  • Watch event: 6
  • Delete event: 30
  • Issue comment event: 2
  • Push event: 283
  • Pull request review comment event: 11
  • Pull request review event: 19
  • Pull request event: 57
  • Create event: 68
Last Year
  • Release event: 25
  • Watch event: 6
  • Delete event: 30
  • Issue comment event: 2
  • Push event: 283
  • Pull request review comment event: 11
  • Pull request review event: 19
  • Pull request event: 57
  • Create event: 68

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 568
  • Total Committers: 13
  • Avg Commits per committer: 43.692
  • Development Distribution Score (DDS): 0.445
Past Year
  • Commits: 68
  • Committers: 4
  • Avg Commits per committer: 17.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Kiran V Garimella k****n@b****g 315
Steve Huang s****g@b****g 99
Jonn Smith j****h 54
BumpVersion Action b****n@g****s 52
bshifaw b****w@b****g 21
Eric Song me@e****o 6
bshifaw b****w@b****m 5
Eric Song s****e@b****g 5
ewanbroad 8****d 4
Bridget Knight 7****t 2
Kiran Garimella k****n@w****g 2
Brian Granger b****r@b****g 2
Ted Sharpe t****e@b****g 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 6 wm8fa-7b6.broadinstitute.org: 1 broadinstitute.com: 1 ericsong.io: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 37
  • Total pull requests: 99
  • Average time to close issues: 7 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 2
  • Total pull request authors: 8
  • Average comments per issue: 1.89
  • Average comments per pull request: 0.14
  • Merged pull requests: 87
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 32
  • Average time to close issues: N/A
  • Average time to close pull requests: about 13 hours
  • Issue authors: 0
  • Pull request authors: 5
  • Average comments per issue: 0
  • Average comments per pull request: 0.09
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • SHuang-Broad (27)
  • kvg (11)
Pull Request Authors
  • jonn-smith (37)
  • kvg (35)
  • SHuang-Broad (29)
  • bshifaw (14)
  • shadizaheri (9)
  • bridgetknight (6)
  • brosula (2)
  • stellaning1120 (1)
  • jamesemery (1)
Top Labels
Issue Labels
wontfix (5) bug (4) good first issue (4) new algo (3) testing (2) new feature (2) documentation (1) tool-specific (1) data QC (1) optimization (1)
Pull Request Labels

Dependencies

.github/workflows/cd.yml actions
  • EndBug/add-and-commit v4 composite
  • JesseTG/rm v1.0.0 composite
  • actions/checkout v2 composite
  • actions/checkout master composite
  • actions/create-release v1 composite
  • actions/setup-python v2 composite
  • christian-draeger/increment-semantic-version 1.0.1 composite
  • christian-draeger/read-properties 1.0.0 composite
  • christian-draeger/write-properties 1.0.1 composite
  • rtCamp/action-slack-notify v2.0.2 composite
.github/workflows/ci_nightly.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • rtCamp/action-slack-notify v2.0.2 composite
.github/workflows/ci_push.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • rtCamp/action-slack-notify v2.0.2 composite
docker/lr-10x/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-align/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-asm/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-basic/Dockerfile docker
  • ubuntu 18.04 build
docker/lr-blast/Dockerfile docker
  • ubuntu 21.04 build
docker/lr-bri/Dockerfile docker
  • ubuntu latest build
docker/lr-c3poa/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-canu/Dockerfile docker
  • openjdk 8 build
docker/lr-cartographer/Dockerfile docker
  • ubuntu 21.04 build
docker/lr-clair/Dockerfile docker
  • ubuntu 16.04 build
docker/lr-cloud-downloader/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-dv/Dockerfile docker
  • google/deepvariant 1.3.0 build
docker/lr-finalize/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-flye/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-gatk/Dockerfile docker
  • us.gcr.io/broad-gatk/gatk latest build
docker/lr-guppy/Dockerfile docker
  • nvidia/cuda 10.2-base-ubuntu16.04 build
docker/lr-hifiasm/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-jupyter/Dockerfile docker
  • jupyter/datascience-notebook latest build
docker/lr-longshot/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-medaka/Dockerfile docker
  • nvidia/cuda 10.1-cudnn7-devel-ubuntu18.04 build
docker/lr-megalodon/Dockerfile docker
  • nvidia/cuda 10.2-base-centos8 build
docker/lr-methylation/Dockerfile docker
  • nvidia/cuda 10.1-cudnn7-devel-ubuntu18.04 build
docker/lr-metrics/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-mosdepth/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-nanoplot/Dockerfile docker
  • python 3.9-buster build
docker/lr-nanopolish/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-ont/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-pacasus/Dockerfile docker
  • nvidia/cuda 10.1-devel-ubuntu16.04 build
docker/lr-pb/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-peregrine/Dockerfile docker
  • cschin/peregrine 0.1.6.1 build
docker/lr-quast/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-racon/Dockerfile docker
  • gpuci/clara-genomics-base cuda10.1-ubuntu18.04-gcc7-py3.5 build
docker/lr-ref/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-seanken/Dockerfile docker
  • dceoy/r-tidyverse latest build
docker/lr-smrttools/Dockerfile docker
  • ubuntu 20.04 build
docker/lr-sniffles2/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-softclipper/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-splicedbam2gff/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-sqanti/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-stringtie2/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-sv/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-svim/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-talon/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-tama/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-transcript_utils/Dockerfile docker
  • ubuntu 20.04 build
docker/lr-utils/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-whatshap/Dockerfile docker
  • continuumio/miniconda3 latest build
docker/lr-winnowmap/Dockerfile docker
  • ubuntu 18.04 build
docker/sr-utils/Dockerfile docker
  • continuumio/miniconda3 latest build
requirements.txt pypi
  • construct *
  • google-cloud-storage *
  • numpy *
  • pysam *
  • pytest *
  • pytest-console-scripts *
  • tinydb *
  • tox *
.github/workflows/git_page.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/validate_dockstore_yaml.yml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • actions/setup-java v2 composite
docker/lr-talon/environment.yml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • bcftools 1.9
  • bedtools 2.30.0
  • bzip2 1.0.8
  • ca-certificates 2021.5.30
  • certifi 2021.5.30
  • curl 7.71.1
  • gsl 2.5
  • htslib 1.9
  • krb5 1.17.2
  • ld_impl_linux-64 2.35.1
  • libblas 3.9.0
  • libcblas 3.9.0
  • libcurl 7.71.1
  • libdeflate 1.2
  • libedit 3.1.20191231
  • libffi 3.2.1
  • libgcc-ng 9.3.0
  • libgfortran-ng 9.3.0
  • libgfortran5 9.3.0
  • libgomp 9.3.0
  • libopenblas 0.3.15
  • libssh2 1.9.0
  • libstdcxx-ng 9.3.0
  • ncurses 6.1
  • openssl 1.1.1k
  • perl 5.32.1
  • pip 21.1.2
  • python 3.6.10
  • python_abi 3.6
  • readline 8.0
  • samtools 1.9
  • setuptools 49.6.0
  • sqlite 3.32.3
  • tk 8.6.10
  • wheel 0.36.2
  • xz 5.2.5
  • zlib 1.2.11
docker/lr-whatshap/environment.yml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • bcftools 1.8
  • blas 1.0
  • bz2file 0.98
  • bzip2 1.0.8
  • c-ares 1.17.1
  • ca-certificates 2021.5.25
  • certifi 2021.5.30
  • curl 7.71.1
  • htslib 1.11
  • krb5 1.18.2
  • ld_impl_linux-64 2.33.1
  • libcurl 7.71.1
  • libdeflate 1.7
  • libedit 3.1.20191231
  • libev 4.33
  • libffi 3.3
  • libgcc 7.2.0
  • libgcc-ng 9.3.0
  • libgfortran-ng 7.3.0
  • libgomp 9.3.0
  • libnghttp2 1.43.0
  • libopenblas 0.3.10
  • libssh2 1.9.0
  • libstdcxx-ng 9.3.0
  • ncurses 6.2
  • nomkl 3.0
  • openblas 0.3.10
  • openblas-devel 0.3.10
  • openssl 1.1.1k
  • pip 21.0.1
  • pyfaidx 0.5.9.5
  • python 3.6.13
  • pyvcf 0.6.8
  • readline 8.1
  • samtools 1.11
  • setuptools 52.0.0
  • six 1.15.0
  • sqlite 3.35.4
  • tk 8.6.10
  • wheel 0.36.2
  • xopen 0.7.3
  • xz 5.2.5
  • zlib 1.2.11
docker/lr-10x/environment.yml pypi
  • biopython *
  • pysam *
docker/lr-align/environment.yml pypi
docker/lr-asm/environment.yml pypi
docker/lr-bri/environment.yml pypi
docker/lr-c3poa/environment.yml pypi
docker/lr-cloud-downloader/environment.yml pypi
  • crcmod ==1.7
docker/lr-finalize/environment.yml pypi
docker/lr-flye/environment.yml pypi
docker/lr-longshot/environment.yml pypi
docker/lr-metrics/environment.yml pypi
docker/lr-mosdepth/environment.yml pypi
docker/lr-ont/environment.yml pypi
docker/lr-pb/environment.yml pypi
docker/lr-peregrine/environment.yml pypi
docker/lr-quast/environment.yml pypi
docker/lr-ref/environment.yml pypi
docker/lr-seanken/environment.yml pypi
docker/lr-sniffles2/environment.yml pypi
docker/lr-stringtie2/environment.yml pypi
docker/lr-sv/environment.yml pypi
docker/lr-tama/environment.yml pypi
docker/lr-utils/environment.yml pypi
docker/sr-utils/environment.yml pypi