umccr/cwl-ica

Issues

• Revisit BCLConvert pipeline

  #564 opened 7 months ago by alexiswl
  3

• Replace `output_directory` and `output_file_prefix` with `output_prefix` for dragen pipelines

  #554 opened 7 months ago by alexiswl
  1

• Add option to set vc-combine-phased-variants-distance in somatic and germline workflows

  #355 opened 2 years ago by mhlunimelb
  5

• Add cttsor step to the cttso post-processing pipeline

  #456 opened 8 months ago by alexiswl
  4

• Add cram input option to samtools fastq pipeline

  #535 opened 8 months ago by alexiswl
  1

• Allow cram inputs into dragen somatic with germline pipeline

  #539 opened 8 months ago by alexiswl
  0

• dragen-somatic-with-germline-pipeline parameter 'vc_target_vaf_somatic' isn't a parameter to the downstream tool

  #464 opened 8 months ago by alexiswl
  0

• Qualimap running out of temp space on ICAv2

  #538 opened 8 months ago by alexiswl
  0

• OOM Error for TN runs on ICAV2

  #536 opened 8 months ago by alexiswl
  0

• Clean up non-ascii characters in dragen docs

  #537 opened 8 months ago by alexiswl
  0

• Update multiqc commands to be ICAv2 compatible

  #497 opened 10 months ago by alexiswl
  0

• interop: imaging_table

  #492 opened 10 months ago by pdiakumis
  0

• Update GH Action user from pipelines-trial to pipelines user

  #498 opened 10 months ago by alexiswl
  0

• Separate out dragen and CPU based bclconvert workflows

  #359 opened a year ago by alexiswl
  1

• Merge tools bcl-convert and BclConvert

  #360 opened a year ago by alexiswl
  1

• Build BCLConvert 4.1.7 workflow

  #373 opened a year ago by alexiswl
  1

• Move out dockstore tags to their own tags (pushed by user)

  #440 opened a year ago by alexiswl
  1

• Use new version of aws-actions/aws-secretsmanager-get-secrets

  #460 opened a year ago by alexiswl
  0

• 1 TB commentary for scratch space is causing JS errors

  #457 opened a year ago by alexiswl
  0

• Add tmpDirMin, to dragen tools.

  #451 opened a year ago by alexiswl
  1

• ctDNA TSO500 workflow: copy several temp files into final Results

  #449 opened a year ago by pdiakumis
  6

• Access tokens need to be 'encrypted / decrypted' before being set by action outputs

  #447 opened a year ago by alexiswl
  0

• HOME dir set to '/' not blank

  #430 opened a year ago by alexiswl
  0

• Sync tools not triggering with change to tj-actions logic

  #429 opened a year ago by alexiswl
  0

• ICAV2-CLI-PLUGINS needs to be installed for the create workflow release asset to be installed

  #433 opened a year ago by alexiswl
  1

• No Writable Envs Dir Error

  #426 opened a year ago by alexiswl
  0

• Changes not in GH action paths are triggering the sync workflows command

  #424 opened a year ago by alexiswl
  0

• Release assets should be pushed to an ICAv2 project AND bundled

  #353 opened a year ago by alexiswl
  0

• Move from epoch to YYYYMMDDHHMMSS format for releases

  #420 opened a year ago by alexiswl
  0

• Use AWS OIDC to collect ICAV2 ACCESS Token for pipeline project

  #422 opened a year ago by alexiswl
  0

• Add hints to workflows to indicate best analysisstoragesize for ICAv2 workflows

  #390 opened a year ago by alexiswl
  1

• production_workflows should be available in the development project

  #402 opened a year ago by alexiswl
  0

• Add analysis output logic into workflows as a schema

  #354 opened a year ago by alexiswl
  1

• Release all production versions

  #404 opened a year ago by alexiswl
  1

• Arriba fusion calling - OOM error

  #333 opened a year ago by skanwal
  9

• Add 'keywords' schema attribute in workflows

  #389 opened 2 years ago by alexiswl
  0

• Enable HRD calling in TN workflow

  #358 opened 2 years ago by skanwal
  3

• Update Arriba to v2.4

  #351 opened 2 years ago by skanwal
  2

• Add bam_input option to dragen transcriptome pipeline

  #348 opened 2 years ago by alexiswl
  0

• Somatic Tool error when using fastq-list-rows

  #343 opened 2 years ago by alexiswl
  0

• Allow umccrise to normal bam file from somatic directory if germline directory does not have a bam file

  #334 opened 2 years ago by alexiswl
  0

• Fix TS7053 Error in Utils

  #325 opened 2 years ago by alexiswl
  0

• UMCCRise workflows inputs dragen-normal-id and dragen-tumor-id should be optional strings

  #328 opened 2 years ago by alexiswl
  0

• Add --enable-map-align parameter in dragen germline and dragen-somatic-with-germline v4 workflows

  #327 opened 2 years ago by alexiswl
  0

• Add additional workflow parameters to umccrise

  #323 opened 2 years ago by alexiswl
  2

• Add v4 workflows to production_workflows project

  #322 opened 2 years ago by alexiswl
  0

• Dragen germline tool error

  #316 opened 2 years ago by skanwal
  7

• umccrise-2.2.0--0 EOF error

  #315 opened 2 years ago by skanwal
  1

• UMCCRISE: make dragen_tumor_id and dragen_normal_id inputs optional

  #312 opened 2 years ago by skanwal
  1

• Umccrise tool breaks if germline and somatic directories have the same basename

  #311 opened 2 years ago by alexiswl
  0