mskcc/pluto-cwl

Issues

• Fix Jenkins recipe

  #113 opened 3 years ago by stevekm
  0

• Need to add `id` and `label` fields to all CWL's and tools

  #114 opened 3 years ago by stevekm
  0

• add CMO ASSAY COVERAGE to data clinical sample

  #109 opened 3 years ago by stevekm
  0

• add CMO PORTAL MUTS to data clinical sample

  #110 opened 3 years ago by stevekm
  0

• fix Pluto serializer script for pairs

  #112 opened 3 years ago by stevekm
  0

• High temp storage usage with samples_fillout_index_batch_workflow.cwl

  #106 opened 3 years ago by stevekm
  1

• add CMO ASSAY label to data clinical sample

  #108 opened 3 years ago by stevekm
  0

• need to update samples fillout workflow output

  #84 opened 3 years ago by stevekm
  4

• consolidate Python fixtures

  #94 opened 3 years ago by stevekm
  3

• incorporate dos2unix into samples fillout workflow (resurrection workflow)

  #70 opened 4 years ago by stevekm
  1

• portal/data_clinical_sample.txt file is missing pipeline version

  #66 opened 4 years ago by timosong
  3

• update workflow.cwl to include more recent pipeline outputs and refactors

  #69 opened 4 years ago by stevekm
  0

• add OncoKB annotation to maf output

  #60 opened 4 years ago by stevekm
  0

• Make data_mutations_uncalled and meta_mutations_uncalled files for cBioPortal

  #63 opened 4 years ago by stevekm
  2

• Add sample vs. cohort plots to reporting

  #47 opened 4 years ago by stevekm
  0

• add sample concordance / discordance comparisons

  #52 opened 4 years ago by stevekm
  0

• pipeline tools documentation for PI's

  #53 opened 4 years ago by stevekm
  1

• get IGV Reports into the workflow

  #43 opened 4 years ago by stevekm
  0

• use .bed file for IGV report sites

  #45 opened 4 years ago by stevekm
  1

• get variant overlap metrics into the pipeline

  #41 opened 4 years ago by stevekm
  2

• add TMB maf output

  #111 opened 10 months ago by stevekm
  0

• fillout maf needs to use updated MafWriter to ensure Amino_Acid_Change column is present

  #116 opened 2 years ago by stevekm
  2

• Update test cases for Jenkins

  #92 opened 3 years ago by stevekm
  3

• documentation for developers

  #55 opened 3 years ago by stevekm
  2

• fix duplicate file output in portal workflow

  #101 opened 3 years ago by stevekm
  2

• Need input & output of related samples for reporting

  #71 opened 3 years ago by stevekm
  1

• switch to a testing framework that supports parallel execution

  #54 opened 3 years ago by stevekm
  4

• Need to get a run metadata samplesheet

  #57 opened 3 years ago by stevekm
  1

• add "print json" method to run script

  #62 opened 3 years ago by stevekm
  2

• update & refactor test cases

  #103 opened 3 years ago by stevekm
  1

• need to scrub sample IDs from demo dataset

  #51 opened 3 years ago by stevekm
  2

• refactor samples_fillout_workflow to use scatter at getbasecountsmultisample step

  #73 opened 3 years ago by stevekm
  1

• remove task failure suppression

  #72 opened 3 years ago by stevekm
  1

• deprecate run.py script

  #77 opened 3 years ago by stevekm
  1

• clean up env.sh

  #78 opened 3 years ago by stevekm
  1

• need to output per-sample portal maf files

  #79 opened 3 years ago by stevekm
  2

• Update test suite for integration testing

  #80 opened 3 years ago by stevekm
  2

• new facets suite container is breaking the workflow

  #68 opened 3 years ago by stevekm
  5

• Need pipeline reports

  #46 opened 4 years ago by stevekm
  4

• Portal files output needs new line (meta_mutations_extended.txt)

  #65 opened 4 years ago by timosong
  2

• Incorporate DMP copy number information (resurrection)

  #64 opened 4 years ago by timosong
  1

• refactor samples fillout methods

  #61 opened 4 years ago by stevekm
  1

• test in pluto

  #67 opened 4 years ago by allanbolipata
  0

• update_cBioPortal_data.py merge_mafs uses too much memory

  #56 opened 4 years ago by stevekm
  3

• Add MSI to the workflow

  #49 opened 4 years ago by stevekm
  1

• IGV reports sort by base

  #48 opened 4 years ago by stevekm
  1

• add more columns to cBio utils module

  #44 opened 4 years ago by stevekm
  2

• create mini test bam files, standardized mini test maf files

  #50 opened 4 years ago by stevekm
  2

• Make ultron_prototype primary CWL for samples fillout workflow

  #42 opened 4 years ago by allanbolipata
  1

• set GetBaseCountsMultiSample to use 4 CPU's

  #39 opened 4 years ago by stevekm
  1