Issues

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

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  mskcc/pluto-cwl#114 · Filter by author stevekm opened on Aug 25, 2022

• Fix Jenkins recipe

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  mskcc/pluto-cwl#113 · Filter by author stevekm opened on Aug 2, 2022

• fix Pluto serializer script for pairs

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  mskcc/pluto-cwl#112 · Filter by author stevekm opened on Aug 2, 2022

• add CMO PORTAL MUTS to data clinical sample

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  mskcc/pluto-cwl#110 · Filter by author stevekm opened on Aug 2, 2022

• add CMO ASSAY COVERAGE to data clinical sample

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  mskcc/pluto-cwl#109 · Filter by author stevekm opened on Aug 2, 2022

• add CMO ASSAY label to data clinical sample

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  mskcc/pluto-cwl#108 · Filter by author stevekm opened on Aug 2, 2022

• High temp storage usage with samples_fillout_index_batch_workflow.cwl

  bughigh priorityrevisit this later
  mskcc/pluto-cwl#106 · Filter by author stevekm opened on Jul 12, 2022
  1

• consolidate Python fixtures

  enhancementlow priorityrevisit this later
  mskcc/pluto-cwl#94 · Filter by author stevekm opened on Jan 25, 2022
  3

• need to update samples fillout workflow output

  enhancementhigh priorityrevisit this later
  mskcc/pluto-cwl#84 · Filter by author stevekm opened on Jan 4, 2022
  4

• incorporate dos2unix into samples fillout workflow (resurrection workflow)

  buglow priorityrevisit this later
  mskcc/pluto-cwl#70 · Filter by author stevekm opened on Sep 8, 2021
  1

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

  enhancementrevisit this later
  mskcc/pluto-cwl#69 · Filter by author stevekm opened on Aug 11, 2021

• portal/data_clinical_sample.txt file is missing pipeline version

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  mskcc/pluto-cwl#66 · Filter by author timosong opened on Jul 27, 2021
  3

• Make data_mutations_uncalled and meta_mutations_uncalled files for cBioPortal

  enhancementhigh priorityrevisit this later
  mskcc/pluto-cwl#63 · Filter by author stevekm opened on Jun 22, 2021
  2

• add OncoKB annotation to maf output

  enhancementhigh priorityrevisit this later
  mskcc/pluto-cwl#60 · Filter by author stevekm opened on May 28, 2021

• pipeline tools documentation for PI's

  low priorityrevisit this later
  mskcc/pluto-cwl#53 · Filter by author stevekm opened on Mar 31, 2021
  1

• add sample concordance / discordance comparisons

  low priorityrevisit this later
  mskcc/pluto-cwl#52 · Filter by author stevekm opened on Mar 31, 2021

• Add sample vs. cohort plots to reporting

  enhancementlow priorityrevisit this later
  mskcc/pluto-cwl#47 · Filter by author stevekm opened on Mar 16, 2021

• use .bed file for IGV report sites

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  mskcc/pluto-cwl#45 · Filter by author stevekm opened on Mar 15, 2021
  1

• get IGV Reports into the workflow

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  mskcc/pluto-cwl#43 · Filter by author stevekm opened on Mar 11, 2021

• get variant overlap metrics into the pipeline

  enhancementrevisit this later
  mskcc/pluto-cwl#41 · Filter by author stevekm opened on Mar 4, 2021
  2

• Add concordance workflow & reporting

  enhancementhigh priorityrevisit this later
  mskcc/pluto-cwl#32 · Filter by author stevekm opened on Jan 14, 2021
  1