Ecosyste.ms: Issues

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GitHub / aws/amazon-genomics-cli issues and pull requests

#612 - chore(deps): bump vm2 from 3.9.11 to 3.9.18 in /scripts

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, javascript

#611 - chore(deps): bump vm2 from 3.9.11 to 3.9.18 in /extras/agc-minimal-permissions

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, javascript

#610 - fix: bump nextflow version to 23.04.1 #609

Pull Request - State: open - Opened by gf-atebbe over 1 year ago

#609 - Update the version of Nextflow used to 23.04.1

Issue - State: open - Opened by gf-atebbe over 1 year ago
Labels: enhancement

#608 - chore(deps): bump vm2 from 3.9.11 to 3.9.17 in /scripts

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#607 - chore(deps): bump vm2 from 3.9.11 to 3.9.17 in /extras/agc-minimal-permissions

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#606 - chore(deps): bump vm2 from 3.9.11 to 3.9.16 in /extras/agc-minimal-permissions

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#605 - chore(deps): bump vm2 from 3.9.11 to 3.9.16 in /scripts

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#604 - Allow The Compute Environment Only to EFS Security Group

Pull Request - State: open - Opened by souravskr over 1 year ago

#602 - chore(deps): bump vm2 from 3.9.11 to 3.9.15 in /scripts

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#601 - chore(deps): bump vm2 from 3.9.11 to 3.9.15 in /extras/agc-minimal-permissions

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#600 - fix: grant GetObject permissions in AgcPermissionStack user policy

Pull Request - State: open - Opened by patmagee over 1 year ago

#599 - Nextflow > 22.04.03 not supported!

Issue - State: open - Opened by MoniDR over 1 year ago
Labels: enhancement

#598 - PATH overwritten on debian-based images using miniwdl

Issue - State: open - Opened by hkeward over 1 year ago
Labels: bug

#597 - Fix: Typo for the TypeScript link description on Website

Pull Request - State: open - Opened by souravskr over 1 year ago

#594 - chore(deps): bump golang.org/x/net from 0.1.0 to 0.7.0 in /packages/cli

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, go

#593 - Native AWS batch support for snakemake

Issue - State: open - Opened by fgypas over 1 year ago
Labels: enhancement

#591 - docs: Update information about EFS throughput (issue-590)

Pull Request - State: closed - Opened by markjschreiber over 1 year ago

#590 - Quantify cost of using EFS provisioned throughput

Issue - State: open - Opened by wleepang over 1 year ago

#589 - Exec format error on Mac M1 with V1.6.0

Issue - State: open - Opened by TSFelg over 1 year ago - 3 comments
Labels: bug, investigating

#588 - chore(deps): bump json5 from 2.2.0 to 2.2.3 in /extras/agc-minimal-permissions

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, javascript

#587 - nf-core/sarek demo doesn't work due to the input validation error

Issue - State: open - Opened by veselovamazon over 1 year ago
Labels: bug

#586 - fix: Update go version

Pull Request - State: closed - Opened by markjschreiber over 1 year ago

#585 - chore(merge-back): 1.6.0

Pull Request - State: closed - Opened by aws-genomics-automation almost 2 years ago

#584 - chore(release): v1.6.0

Pull Request - State: closed - Opened by aws-genomics-automation almost 2 years ago

#583 - fix: Default to undefined

Pull Request - State: closed - Opened by m3talsmith almost 2 years ago

#582 - fix: Allow null kms decrypt policy

Pull Request - State: closed - Opened by m3talsmith almost 2 years ago

#581 - feat: Cross Account KMS

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#580 - codon172 adding .agcingore file

Pull Request - State: closed - Opened by hnookalaaws almost 2 years ago

#579 - Add support for minvcpu and desiredvCpus to context

Issue - State: open - Opened by KevinSayers almost 2 years ago
Labels: enhancement

#578 - chore: Update snakemake demo to work with snakemake v7.18.2

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#577 - Workflow definitions that include a `workflow.zip` file fail parsing in CromwellWESAdapter

Issue - State: open - Opened by wleepang almost 2 years ago - 1 comment
Labels: bug

#576 - Support using custom images from public repository

Issue - State: open - Opened by mattcarp12 almost 2 years ago
Labels: enhancement

#575 - fix: Install script output name

Pull Request - State: closed - Opened by m3talsmith almost 2 years ago - 1 comment

#574 - AGC not working with enforced S3 encryption

Issue - State: open - Opened by ArlindNocaj almost 2 years ago
Labels: bug

#573 - ecr:SetRepositoryPolicy missing for account activate with minimum permissions

Issue - State: open - Opened by ArlindNocaj almost 2 years ago - 1 comment
Labels: bug

#572 - Updated cromwell version to Loka(83.1-AWS)

Pull Request - State: closed - Opened by hnookalaaws almost 2 years ago

#571 - feat: Add resource tags that indicate engine used by context

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#570 - Workflow running out of memory

Issue - State: open - Opened by spitfiredd almost 2 years ago - 5 comments
Labels: bug

#569 - feat: Add ARM support for CLI build

Pull Request - State: closed - Opened by m3talsmith almost 2 years ago

#568 - chore: Add EC2 Service Endpoint to AGC created VPCs

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#567 - agc context deploy not rebuilding workflow.zip file

Issue - State: open - Opened by spitfiredd almost 2 years ago - 2 comments
Labels: bug

#566 - chore: Add vscode devcontainer

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#565 - fix: AGC run fails when empty strings in inputs.json file

Pull Request - State: closed - Opened by mattcarp12 almost 2 years ago

#564 - docs: Migrate remaining pages to Hugo page bundles

Pull Request - State: closed - Opened by markjschreiber almost 2 years ago

#563 - chore: Update miniwdl version to match miniwdl AWS plugin that supports curr…

Pull Request - State: closed - Opened by chinjsg almost 2 years ago - 2 comments

#562 - docs: Added architecture diagrams

Pull Request - State: closed - Opened by markjschreiber almost 2 years ago

#561 - Bump npm packages

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#560 - Npm audit fix to update minimatch in dependency chain

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#559 - Update minimatch to patch CVE-2022-3517

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#558 - Nodejs LTS repo update

Pull Request - State: open - Opened by arupgsh almost 2 years ago - 2 comments

#557 - chore(release): v1.6.0

Pull Request - State: closed - Opened by aws-genomics-automation almost 2 years ago

#556 - Update go versions to 1.9 in go mod

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#555 - Merge pull request #551 from aws/vishnuvalleru/set-rnaseq-version-v1_2

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#554 - Upgrade fails from 1.5.0 to 1.5.2

Issue - State: closed - Opened by bounlu almost 2 years ago - 2 comments
Labels: bug

#553 - chore(merge-back): 1.5.2

Pull Request - State: closed - Opened by aws-genomics-automation almost 2 years ago

#552 - Add warning if a local work dir is found

Issue - State: open - Opened by KevinSayers almost 2 years ago - 2 comments
Labels: enhancement

#551 - Set example worklfow, nextflow-io rnaseq to v1.2

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#550 - Update prerequisites.md

Pull Request - State: closed - Opened by mepowers almost 2 years ago

#547 - AGC run fails when empty strings in inputs.json file

Issue - State: open - Opened by biofilos almost 2 years ago - 4 comments
Labels: bug

#546 - Update cdk go version

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#545 - Add support for cross account SSE-KMS S3 buckets

Issue - State: open - Opened by giany almost 2 years ago - 1 comment
Labels: enhancement

#544 - Add support for specifying CPU for Snakemake head job

Issue - State: open - Opened by KevinSayers almost 2 years ago
Labels: enhancement

#541 - Snakemake bug when mainWorkflowURL is github repo

Issue - State: open - Opened by KevinSayers almost 2 years ago
Labels: bug

#540 - Snakemake and singularity

Issue - State: open - Opened by diegovevo almost 2 years ago - 1 comment
Labels: bug

#539 - chore(release): 1.5.2

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#536 - Enforce vm2 version to be >=3.9.11

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#535 - Remove the default security group from the AGC generated VPC

Issue - State: open - Opened by markjschreiber almost 2 years ago - 2 comments
Labels: enhancement

#534 - Default AGC bucket should remove the possibility of public access

Issue - State: open - Opened by markjschreiber almost 2 years ago
Labels: enhancement

#533 - Add EC2 Service Endpoint to AGC created VPCs

Issue - State: open - Opened by markjschreiber almost 2 years ago
Labels: enhancement, good first issue

#532 - Add option to enable container insights on batch compute environments

Issue - State: open - Opened by markjschreiber almost 2 years ago
Labels: enhancement

#531 - Ensure worker EC2 instances run Instance Metadata Service V2

Issue - State: open - Opened by markjschreiber almost 2 years ago
Labels: enhancement

#528 - Update CDK to pickup latest vm2

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#526 - Remove spot context from Integration tests

Pull Request - State: closed - Opened by vvalleru almost 2 years ago

#523 - fix: Revision tag in Nextflow rnaseq example

Pull Request - State: closed - Opened by KevinSayers about 2 years ago - 1 comment

#507 - feat: support for PRIVATE API Gateway endpoints

Pull Request - State: closed - Opened by markjschreiber about 2 years ago - 1 comment

#482 - "results" folder not stored when using nextflow engine

Issue - State: open - Opened by MrOlm over 2 years ago - 1 comment
Labels: bug

#474 - --inputsFile is not being passed to miniwdl run

Issue - State: open - Opened by nh13 over 2 years ago - 13 comments
Labels: bug

#414 - feat: allows skipping of specific nextflow files from being cached

Pull Request - State: open - Opened by OhCloud over 2 years ago - 1 comment

#394 - Consistently Tag Engine Batch jobs

Issue - State: open - Opened by markjschreiber over 2 years ago - 1 comment
Labels: enhancement

#393 - ARM support for install.sh

Issue - State: open - Opened by bollig over 2 years ago - 4 comments
Labels: enhancement, closed-for-staleness

#381 - Explore TCP kernel flags to improve worker EC2 I/O reliability

Issue - State: closed - Opened by markjschreiber over 2 years ago - 3 comments
Labels: enhancement

#331 - fix: Revert snakemake code to help with release

Pull Request - State: closed - Opened by waliag87 over 2 years ago

#301 - fix: fix retry logic for ecs-additions

Pull Request - State: closed - Opened by a-li over 2 years ago - 1 comment

#249 - chore(merge-back): 1.1.2

Pull Request - State: closed - Opened by aws-genomics-automation almost 3 years ago - 1 comment

#226 - chore(merge-back): 1.1.2

Pull Request - State: closed - Opened by aws-genomics-automation almost 3 years ago

#197 - fix: returning default config with initial email config

Pull Request - State: closed - Opened by anisatahlil almost 3 years ago - 1 comment

#154 - feat: Added default format flag

Pull Request - State: closed - Opened by anisatahlil almost 3 years ago - 4 comments

#144 - feat: timeout for context and core deployments

Pull Request - State: closed - Opened by abassyiouni almost 3 years ago - 2 comments

#112 - docs: Test PR. Add whitespace

Pull Request - State: closed - Opened by a-li almost 3 years ago

#107 - fix: Shows an error if the logs can't be retrieved - IGNORE THIS PR.

Pull Request - State: closed - Opened by a-li almost 3 years ago

#105 - fix: Shows an error if the logs can't be retrieved

Pull Request - State: closed - Opened by a-li almost 3 years ago

#104 - fix: Shows an error if the logs can't be retrieved. IGNORE THIS PR.

Pull Request - State: closed - Opened by a-li almost 3 years ago