epruesse/ymp

Issues

• Show path in missing path resource exception

  #169 opened 4 months ago by epruesse
  0

• verify stage name length

  #173 opened 3 years ago by epruesse
  0

• allow copying out built-in stages

  #172 opened 3 years ago by epruesse
  0

• Environments install with outdated spec file if env desc changed

  #171 opened 3 years ago by epruesse
  0

• Don't override dict/list with none in config

  #170 opened 3 years ago by epruesse
  0

• Fix generating canned environments

  #114 opened 4 years ago by epruesse
  0

• Replace "ALL" with project name

  #156 opened 4 years ago by epruesse
  0

• Allow parametrizing pipelines

  #126 opened 4 years ago by epruesse
  1

• Allow capping number of threads

  #123 opened 4 years ago by epruesse
  1

• Allow pipeline override of rule parameters

  #127 opened 4 years ago by epruesse
  1

• Allow capping and scaling resources

  #152 opened 4 years ago by epruesse
  1

• Get rid of all_targets.stamp

  #150 opened 4 years ago by epruesse
  0

• Add scattering stages (MAG generation)

  #81 opened 4 years ago by epruesse
  1

• Ensure that id columns do not contain bad characters

  #145 opened 4 years ago by epruesse
  0

• Allow hiding internal pipeline outputs

  #125 opened 4 years ago by epruesse
  0

• Dependabot couldn't authenticate with https://pypi.python.org/simple/

  #131 opened 4 years ago by dependabot-preview
  0

• Implement implicit stages

  #72 opened 4 years ago by epruesse
  1

• Fix pushing to pypi

  #115 opened 4 years ago by epruesse
  1

• Allow overriding built-in stages

  #124 opened 4 years ago by epruesse
  0

• Validate config

  #113 opened 4 years ago by epruesse
  1

• Validate and document config YAML

  #32 opened 7 years ago by epruesse
  0

• Build stage in normalized location

  #73 opened 6 years ago by epruesse
  1

• Docs failing due to conda out of memory

  #80 opened 4 years ago by epruesse
  0

• Verify installed snakemake version at startup

  #51 opened 4 years ago by epruesse
  0

• nohup option removes coloring

  #34 opened 4 years ago by epruesse
  0

• Error downloading qt5.9.7 when trying to install/make certain stages

  #89 opened 4 years ago by hhollandmoritz
  4

• The name of the ymp.yml file

  #88 opened 5 years ago by hhollandmoritz
  3

• Complete Tab Expansion

  #38 opened 6 years ago by epruesse
  0

• Persistent add_rule bug prevents running any commands

  #79 opened 6 years ago by hhollandmoritz
  7

• implement retry for downloader

  #61 opened 6 years ago by epruesse
  0

• Auto-Generate Stage Tests

  #71 opened 6 years ago by epruesse
  1

• Add StageGroups and IOTypes

  #33 opened 6 years ago by epruesse
  0

• Stagify indexing?

  #62 opened 6 years ago by epruesse
  0

• Handle alternative URLs for environments

  #64 opened 6 years ago by epruesse
  0

• Handle abort during env download

  #68 opened 6 years ago by epruesse
  1

• docs: highlight `{: :}` with pygments

  #37 opened 7 years ago by epruesse
  0

• Add Kallisto / Salmon

  #65 opened 6 years ago by epruesse
  0

• support singularity

  #55 opened 7 years ago by epruesse
  0

• Add SRA downloading test case

  #52 opened 7 years ago by epruesse
  0

• show localrules flag in docs

  #36 opened 7 years ago by epruesse
  0

• show ruleorder in docs

  #35 opened 7 years ago by epruesse
  0

• Implement "csv" string expansion

  #29 opened 7 years ago by epruesse
  0

• v0.2.0 - second bioconda

  #70 opened 6 years ago by epruesse
  0

• Have ymp init detect available memory

  #69 opened 6 years ago by epruesse
  1

• Add RSEM

  #40 opened 7 years ago by epruesse
  0

• Add STAR

  #41 opened 7 years ago by epruesse
  0

• Unit-tests conda env too big

  #31 opened 7 years ago by epruesse
  0

• Move data files to root

  #30 opened 7 years ago by epruesse
  0

• Make YmpConfigError message more helpful

  #50 opened 7 years ago by epruesse
  1

• ymp env activate bug

  #42 opened 7 years ago by shafferm
  1