Issues

• Installation fails with python 3.12

  PMCC-BioinformaticsCore/janis-core#121 · Filter by author ddeepwell opened on Jan 26, 2024

• Some package dependencies are out of date

  PMCC-BioinformaticsCore/janis-core#120 · Filter by author ddeepwell opened on Jan 16, 2024

• Failed translation of Galaxy tool with ID containing a macro

  PMCC-BioinformaticsCore/janis-core#119 · Filter by author ddeepwell opened on Jan 16, 2024

• Failed translation of Galaxy tool with output collections containing data with same name

  PMCC-BioinformaticsCore/janis-core#118 · Filter by author ddeepwell opened on Jan 16, 2024

• ModuleNotFoundError: No module named 'cwl_utils.parser_v1_2'

  PMCC-BioinformaticsCore/janis-core#105 · Filter by author ntachukwu opened on Nov 17, 2021
  1

• fromwdl: missing optional inputs should result in empty conversion of WDL expressions, not half-empty strings with "null" inside

  PMCC-BioinformaticsCore/janis-core#97 · Filter by author mr-c opened on Aug 30, 2021
  2

• CWL generation: invalid result with output_type=File(), selector=Stdout() → "outputEval: _stderr"

  PMCC-BioinformaticsCore/janis-core#95 · Filter by author mr-c opened on Aug 30, 2021
  1

• fromwdl: can't handle single character identifiers

  PMCC-BioinformaticsCore/janis-core#92 · Filter by author mr-c opened on Aug 30, 2021
  1

• convert to WDL: force co-localization of secondary_files

  PMCC-BioinformaticsCore/janis-core#90 · Filter by author mr-c opened on Aug 26, 2021
  2

• Translation for array of array of file

  PMCC-BioinformaticsCore/janis-core#67 · Filter by author junyk opened on Feb 16, 2021
  3

• Janis is not creating secondary output in WDL for array of outputs in tool

  PMCC-BioinformaticsCore/janis-core#62 · Filter by author illusional opened on Jan 29, 2021

• Add "all-in-one" mechanism to janis translate

  PMCC-BioinformaticsCore/janis-core#60 · Filter by author illusional opened on Jan 27, 2021

• Add ReadJsonOperator

  PMCC-BioinformaticsCore/janis-core#59 · Filter by author illusional opened on Jan 26, 2021

• Allow Stdout / stderr to better participate in operations

  PMCC-BioinformaticsCore/janis-core#58 · Filter by author illusional opened on Jan 26, 2021

• Conditionals' switches do not always work if one of the step input files requires assert_not_null()

  PMCC-BioinformaticsCore/janis-core#36 · Filter by author rlupat opened on Jul 4, 2020
  3

• Janis should throw an error if it detects two tools of same ID+version but are different

  PMCC-BioinformaticsCore/janis-core#32 · Filter by author illusional opened on Jun 18, 2020

• Implicit dependencies

  PMCC-BioinformaticsCore/janis-core#25 · Filter by author illusional opened on May 25, 2020
  2

• Produce a BashTool

  PMCC-BioinformaticsCore/janis-core#20 · Filter by author illusional opened on Apr 21, 2020