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GitHub / aws-samples / aws-genomics-workflows

Genomics Workflows on AWS

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aws-samples%2Faws-genomics-workflows

Stars: 139
Forks: 109
Open Issues: 0

License: mit-0
Language: Shell
Repo Size: 12.4 MB
Dependencies: 1,145

Created: over 5 years ago
Updated: 3 months ago
Last pushed: 10 months ago
Last synced: 2 months ago

Topics: aws, batch, genomics, step-functions, workflows

Files

Readme

Dependencies

environment.yaml pypi

cfn-lint *
fontawesome-markdown ==0.2.6
mkdocs ==1.0.4
mkdocs-macros-plugin ==0.2.4
mkdocs-markdownextradata-plugin ==0.0.5
mkdocs-material ==3.1.0
pymdown-extensions ==6.0

src/aws-genomics-cdk/package.json npm

@aws-cdk/assert 1.128.0 development
@types/node 16.11.0 development
aws-cdk 1.128.0 development
ts-node ^10.3.0 development
typescript ~4.4.4 development
@aws-cdk/aws-batch ^1.128.0
@aws-cdk/aws-ec2 ^1.128.0
@aws-cdk/aws-stepfunctions ^1.128.0
@aws-cdk/aws-stepfunctions-tasks ^1.128.0
@aws-cdk/core 1.128.0
source-map-support ^0.5.20

src/containers/nextflow/Dockerfile docker

public.ecr.aws/seqera-labs/nextflow ${VERSION} build

src/containers/samtools/Dockerfile docker

public.ecr.aws/lts/ubuntu 18.04 build

src/gwf-core-codepipeline/package.json npm

@aws-cdk/assert ^1.127.0 development
@types/jest ^26.0.10 development
@types/node 10.17.27 development
aws-cdk ^1.127.0 development
jest ^27.2.5 development
ts-jest ^26.2.0 development
ts-node ^9.0.0 development
typescript ~3.9.7 development
@aws-cdk/aws-codebuild ^1.127.0
@aws-cdk/aws-codepipeline ^1.127.0
@aws-cdk/aws-codepipeline-actions ^1.127.0
@aws-cdk/core ^1.127.0
source-map-support 0.5.16

requirements.txt pypi

cfn-lint *
fontawesome-markdown ==0.2.6
mkdocs ==1.3.0
mkdocs-macros-plugin ==0.2.4
mkdocs-markdownextradata-plugin ==0.0.5
mkdocs-material ==3.1.0
pymdown-extensions ==6.0

src/lambda/codebuild/requirements.txt pypi

crhelper *

src/lambda/ecr/requirements.txt pypi

cfnresponse *

.github/workflows/gh-pages.yml actions

actions/checkout v2 composite
actions/setup-python v3.1.2 composite
peaceiris/actions-gh-pages v3 composite

.github/workflows/stale.yml actions

actions/stale v5 composite

.github/workflows/test.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v3.1.2 composite

src/aws-genomics-cdk/containers/bwa/Dockerfile docker

public.ecr.aws/lts/ubuntu 18.04 build

src/aws-genomics-cdk/containers/fastqc/Dockerfile docker

ubuntu xenial build

src/aws-genomics-cdk/containers/gatk/Dockerfile docker

broadinstitute/gatk 4.1.3.0 build

src/aws-genomics-cdk/containers/minimap2/Dockerfile docker

ubuntu 18.04 build

src/aws-genomics-cdk/containers/picard/Dockerfile docker

broadinstitute/picard latest build

src/aws-genomics-cdk/containers/samtools/Dockerfile docker

public.ecr.aws/lts/ubuntu 18.04 build

src/containers/bcftools/Dockerfile docker

public.ecr.aws/lts/ubuntu 18.04 build

src/containers/bwa/Dockerfile docker

public.ecr.aws/lts/ubuntu 18.04 build

src/gwf-core-codepipeline/package-lock.json npm

547 dependencies

src/aws-genomics-cdk/package-lock.json npm

541 dependencies