* increase disk size for MakeOptionalBam

* changelogs and pipeline versions

Co-authored-by: Nikelle Petrillo <[email protected]>

* Point fingerprinting file keys to publicly available files

* Remove redundant input files from germline single sample pipeline

* Update Skylab STAR Dockerfile to use Alpine Linux image and remove unneeded packages

* Create build script, version file, and readme for STAR Docker image

* Update StarAlign.wdl to use new STAR docker image

* Update changelogs

* Add --platform flag to STAR Dockerfile

…other ARM machines and fix typos (#777)

* Update ValidateATAC.wdl and ValidateSCATAC.wdl to use Broad samtools image

* Remove redundant samtools Dockerfile and directory

* Remove skylab/hca_adapter directory

* Remove unused TagGeneExon.wdl

* Remove dropseq_tools Docker directories and additional files

Change memory allocation and enable maxRetries in fastp and groupbyUMIs tasks. Temporarily add monitoring scripts to these tasks to monitor memory usage. 
Update the transcriptome bam to be the RSEM post-processed one.
Removing tdr_staging_bucket from test file since it is no longer an input

Co-authored-by: M. Morgan Taylor <[email protected]>
Co-authored-by: Nikelle Petrillo <[email protected]>

* Update imputation bcf/vcftools and minimac4 docker images

* Update changelogs

* Rewrite TrimAdapters Dockerfile, build script
* Create TrimAdapters version list, readme
* Replace TrimAdapters.wdl runtime docker URL with GCR URL
* Rename trim-adapters to ea-utils, push a new image to GCR, and replace all docker image URLs
* Update changelog and version number
* Minor corrections to Minimac4 version list and STAR readme

Remove umi-tools docker directory

* Update Optimus MergeStarOutput task, LoomUtils.wdl tasks to use new pytools docker image

* Standardize paths to scripts in docker image in affected tasks

* Add Docker image files for new pytools docker and reorganize scripts

* Fix print function syntax in scATAC MakeCompliantBAM task

* Update changelogs and version numbers

* Remove old Dockerfiles, build scripts, requirements files

* Revert some changes from #687 in create_snrna_optimus.py to fix a runtime error

* Create new bwa and snaptools-bwa docker files and documentation

* Build images and replace URLs in tasks

* Document pytools docker scripts, remove unused create-npz-output.py script and ConvertStarOutput task

* Update changelogs

* Update bcf/vcftools docker files

* update get_changed_pipeline_worklow_test_args.sh

* Test

* remove Test

…with additionally added required parameter

* update WGS pipeline docs

* Update README.md

* Update website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md

Co-authored-by: ekiernan <[email protected]>

* Rebuild featureCounts image into a general subread image, add documentation and docker files, and update changelogs and URL in tasks

…tute/warp into BroadInternalArraysImputation

…ngle sample

* Update tasks using ubuntu images to use alpine-bash and update changelogs

* Add troubleshooting/standalone run instructions to docker directory readme file

…tute/warp into BroadInternalArraysImputation

…ngle sample

…tute/warp into BroadInternalArraysImputation

…it date

…tion

update tasks with new docker image, update calls to ingesttotdr task …

*run all pipelines in smart tests

* Create new docker files and update tasks and changelogs

…gelogs, and version numbers (#822)

* Correct test string and update testing framework script

#829)

* Remove /cromwell_root/ prefix in file paths and update changelogs

#827)

* Consistency and formatting improvements

* Update some tasks to use rebuilt images

* Update changelogs

…DL (#830)

* Checkpoint. Renamed the package and made modifications based on recommendations in Warp's docker style guide. Local build currently fails even without modifications, currently investigating why.

* Modifications based on WARP's docker style guide

* Updated to conform to the docker style guide of warp. Also upgraded to a more recent Debian version (Bullseye) so tini is part of apt. An upgrade of python was attempted too but pip failed as it can't find old versions of libraries listed in requirements.txt.

* Parameterizing STAR version.

* Adding build script

* Updating build script to push to GCR.

* Changed the WDL to utilize the new container.

* Changing biotypes type from String to File so it localizes.

* Fixing the PATH, rebuilding the container, then setting the WDL to use the new build.

* Ran into an error where STAR was looking for a fasta file that didn't exist. This fixes that error.

* Added Readme for the container.

* Updated changelog and version.

* Changing the list of versions to match the other containers' format

…833)

BroadInternalArrays and BroadInternalImputation: change docker from dockerhub to gcr

dev -> staging