icgc-argo-workflows/data-processing-utility-tools

Issues

• Payload generation tool for RNA-Seq QC metrics

  #134 opened 3 years ago by lindaxiang
  1

• change `data_subtype` to `data_subtypes` and accommodate multiple values

  #121 opened 4 years ago by junjun-zhang
  1

• Change dataType from `Analysis QC` to `Sample QC` for `Cross Sample Contamination` metrics

  #125 opened 3 years ago by lindaxiang
  0

• Consider change dataType from `Analysis QC` to `Sample QC` for `Ploidy` and `Tumour Purity` data subtypes

  #127 opened a year ago by junjun-zhang
  0

• Payload generation tool for RNA-Seq alignment

  #133 opened 3 years ago by lindaxiang
  1

• Update payload-gen-dna-seq-qc tool

  #116 opened 4 years ago by lindaxiang
  1

• Update payload-gen-variant-calling tool

  #118 opened 4 years ago by lindaxiang
  2

• update payload-gen-dna-alignment add support to pass on `info`, add `data_subtypes`

  #120 opened 4 years ago by junjun-zhang
  1

• payload-gen-rna-seq-alignment tool adjustment for STAR outputs to include transcriptome BAM

  #162 opened a year ago by lindaxiang
  1

• Remove metrics section from variant calling `qc_metrics` payloads

  #167 opened 2 years ago by lindaxiang
  1

• Data submission payload check against sample registration

  #161 opened 2 years ago by edsu7
  4

• Detect RNA-seq strandedness in FASTQ

  #153 opened 2 years ago by edsu7
  1

• add installation of procsps in Dockerfile for `payload-gen-seq-experiment`

  #128 opened 4 years ago by junjun-zhang
  1

• Update payload-gen-read-group-ubam

  #117 opened 4 years ago by lindaxiang
  1

• Bug: fix typo in data type Mutect2 Callabe Stats

  #96 opened 4 years ago by junjun-zhang
  1

• Bug: date string (yyyymmdd) in all file names within one song payload must be the same

  #93 opened 4 years ago by junjun-zhang
  1

• improvement: make payload gen tools cacheable

  #90 opened 4 years ago by junjun-zhang
  1

• update payload-gen-dna-seq-qc to sync with seq-data-to-lane-bam 0.3.1.0

  #91 opened 4 years ago by junjun-zhang
  1

• update prep-mutect2-qc to include mutect2 filtering stats and mutect callable stats

  #87 opened 4 years ago by junjun-zhang
  1

• payload-gen-dna-seq-qc needs to be sync'd with seq-data-to-lane-bam for lane bam name

  #75 opened 4 years ago by junjun-zhang
  2

• improvement: use python:3.7.9 as base docker image for prep-mutect2-qc and payload-gen-variant-calling

  #84 opened 4 years ago by junjun-zhang
  1

• verify whether current payload-gen-variant-calling is able to use for mutect2 payloads

  #80 opened 4 years ago by junjun-zhang
  1

• qc preparation for gatk contamination report

  #79 opened 4 years ago by junjun-zhang
  1

• Update the workflow song payload generation step to include session_id

  #72 opened 5 years ago by rosibaj
  1

• 🐛 typo 'Qualitiy Control Metrics' in 'payload-gen-variant-calling'

  #73 opened 5 years ago by junjun-zhang
  1