Code

TB Pipeline on Amazon Genomics CLI#24

Code

Open

mmueller76 wants to merge 60 commits intoPathogen-Genomics-Cymru:mainPathogen-Genomics-Cymru/lodestone:mainfrom mmueller76:tb-pipeline-agcmmueller76/tb-pipeline:tb-pipeline-agcCopy head branch name to clipboard

+610-23

Commits

Commits on Sep 26, 2022

• agc-project.yaml added

  mmueller76

  committed
  72066c3

  Copy full SHA for 72066c3

Commits on Sep 28, 2022

• AGC context name changed

  mmueller76

  committed
  ee7d1f2

  Copy full SHA for ee7d1f2

• agc profile added to nextflow.config

  mmueller76

  committed
  fb1dd53

  Copy full SHA for fb1dd53

• AGC MANIFEST and inputs.json for test scenario1 added

  mmueller76

  committed
  f2dd0e7

  Copy full SHA for f2dd0e7

• test manifest and input.json moved to test/agc

  mmueller76

  committed
  28006bf

  Copy full SHA for 28006bf

Commits on Sep 30, 2022

• input.json added and MANIFEST.json modified for full workflow run

  mmueller76

  committed
  4fdad13

  Copy full SHA for 4fdad13

• python script to generate test scenario is being added

  omrkha

  committed
  e7412e3

  Copy full SHA for e7412e3

• fixed input file path bug in software-json.py

  mmueller76

  committed
  5dd02c7

  Copy full SHA for 5dd02c7

• make singularity directory a workflow input

  mmueller76

  committed
  324b66f

  Copy full SHA for 324b66f

• make resources worklow input

  mmueller76

  committed
  7a4f76f

  Copy full SHA for 7a4f76f

• white space change

  mmueller76

  committed
  50de0d0

  Copy full SHA for 50de0d0

• remove resources from project

  mmueller76

  committed
  5de881a

  Copy full SHA for 5de881a

• tests-scenario-script.py removed

  mmueller76

  committed
  f3442e4

  Copy full SHA for f3442e4

• add build_and_push.sh script to build Docker containers and push them to ECR

  mmueller76

  committed
  6952490

  Copy full SHA for 6952490

Commits on Oct 2, 2022

• made resources input of clockwork workflow

  mmueller76

  committed
  008145d

  Copy full SHA for 008145d

• pull_and-push.sh script to push Docker containers to ECR added

  mmueller76

  committed
  e501286

  Copy full SHA for e501286

Commits on Oct 3, 2022

• fix binary name in gnomon process

  mmueller76

  committed
  4dbff96

  Copy full SHA for 4dbff96

• use Docker containers in ECR

  mmueller76

  committed
  e8fe6a7

  Copy full SHA for e8fe6a7

• script to upload resources (bowtie index, KrakenDB and resouces contained in project to S3

  mmueller76

  committed
  6f3a482

  Copy full SHA for 6f3a482

Commits on Oct 4, 2022

• agc added to profile section of help message

  mmueller76

  committed
  14b4199

  Copy full SHA for 14b4199

Commits on Oct 6, 2022

• defaultCtx name changed to ondemand

  mmueller76

  committed
  fa36883

  Copy full SHA for fa36883

• tag construction in build_and_push.sh refactored

  mmueller76

  committed
  9f36818

  Copy full SHA for 9f36818

• report, trace, timeline and dag generation added to nextflow.config; resources_dir parameter removed from nextflow.config; public preporcessing container replaced with ECR version

  mmueller76

  committed
  793f243

  Copy full SHA for 793f243

• output_dir param removed from testing.config

  mmueller76

  committed
  df9f7ad

  Copy full SHA for df9f7ad

Commits on Oct 12, 2022

• fixed gnomonicus JSON output file name

  mmueller76

  committed
  b0dc499

  Copy full SHA for b0dc499

• changed configuration of report, timeline, trace and dag generation

  mmueller76

  committed
  5600c84

  Copy full SHA for 5600c84

• updated script to provision resources

  mmueller76

  committed
  b236cfd

  Copy full SHA for b236cfd

• kraken_db and bowtie2_index parameters in testing.config updated

  mmueller76

  committed
  bac7e3d

  Copy full SHA for bac7e3d

Commits on Oct 26, 2022

• script to submit test workflow runs

  omrkha

  committed
  b5df9ba

  Copy full SHA for b5df9ba

• script to upload resources to s3 finalised

  omrkha

  committed
  fa0bbb2

  Copy full SHA for fa0bbb2

• output file parameter added to test scenarios generation

  omrkha

  committed
  ac8a2c9

  Copy full SHA for ac8a2c9

Commits on Oct 28, 2022

• session ID added to runtime report

  mmueller76

  committed
  36550b7

  Copy full SHA for 36550b7

• typo in context name in agc-project.yaml fixed

  mmueller76

  committed
  99be17a

  Copy full SHA for 99be17a

• workflow.sessionId added to output directory path

  mmueller76

  committed
  638c1f0

  Copy full SHA for 638c1f0

• defaultCtx removed from AGC project YAML

  mmueller76

  committed
  3ccdcab

  Copy full SHA for 3ccdcab

• tidy up dryrun-test-agc script

  mmueller76

  committed
  83b7506

  Copy full SHA for 83b7506

• renamed ash-script-workflow.sh -> dryrun-test-agc.sh

  mmueller76

  committed
  b469dd5

  Copy full SHA for b469dd5

• fixed indentation in main.nf

  mmueller76

  committed
  ee033ae

  Copy full SHA for ee033ae

• cleaned up provision_resources.sh script

  mmueller76

  committed
  08d5c99

  Copy full SHA for 08d5c99

Commits on Nov 2, 2022

• merge conflict in modules/vcfpredictModules.nf resolved

  mmueller76

  committed
  1fb0696

  Copy full SHA for 1fb0696

Commits on Nov 3, 2022

• made python scripts executable and updated script path in modules

  mmueller76

  committed
  8a76832

  Copy full SHA for 8a76832

• make Nextflow execution report path configurable

  mmueller76

  committed
  7e296b0

  Copy full SHA for 7e296b0

• deleted tests/agc/MANIFEST.scenario1.json

  mmueller76

  committed
  cc70ebf

  Copy full SHA for cc70ebf

• refactored tests/agc/generate-test-scenario-inputs.py

  mmueller76

  committed
  0c146ce

  Copy full SHA for 0c146ce

• consolidated tests/agc/generate-test-scenario-inputs.py and dryrun-test-agc.sh into dryrun-test-agc.py

  mmueller76

  committed
  f9c271e

  Copy full SHA for f9c271e

• resources directory add back into project directory

  mmueller76

  committed
  e68eedd

  Copy full SHA for e68eedd

Commits on Nov 4, 2022

• workflow sessionId removed from output path

  mmueller76

  committed
  06e061c

  Copy full SHA for 06e061c

• worklfow run submission command in dry run script fixed

  mmueller76

  committed
  953c7ad

  Copy full SHA for 953c7ad

• scenarios uncommented

  mmueller76

  committed
  dbfa697

  Copy full SHA for dbfa697

• resources_dir and container_registry params added to nextflow.config

  mmueller76

  committed
  99e602f

  Copy full SHA for 99e602f

• container_registry param added to inputs.json

  mmueller76

  committed
  7503bf4

  Copy full SHA for 7503bf4

• resources_dir and container_registry added to main.nf

  mmueller76

  committed
  3561f7c

  Copy full SHA for 3561f7c

• refactored provision_resources.sh script

  mmueller76

  committed
  82cc05a

  Copy full SHA for 82cc05a

• data section removed from agc-project.yaml file

  mmueller76

  committed
  3e6a825

  Copy full SHA for 3e6a825

• AGC section added to README.md

  mmueller76

  committed
  3e9104f

  Copy full SHA for 3e9104f

• inputs.json templated

  mmueller76

  committed
  2c78db1

  Copy full SHA for 2c78db1

• changes in testing.config reverted

  mmueller76

  committed
  6dd9483

  Copy full SHA for 6dd9483

• kraken_db and bowtie2_index params add to dryrun-test-agc.py

  mmueller76

  committed
  8f633a9

  Copy full SHA for 8f633a9

• output_dir reinstated in testing.config

  mmueller76

  committed
  f19ec2b

  Copy full SHA for f19ec2b

• white space change testing.config

  mmueller76

  committed
  2f03654

  Copy full SHA for 2f03654