PMCC-BioinformaticsCore janis-core issues

PMCC-BioinformaticsCore / janis-core

Core python modules for Janis Pipeline workflow assistant

GNU General Public License v3.0

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Installation fails with python 3.12

#121 ddeepwell opened 9 months ago
0
Some package dependencies are out of date

#120 ddeepwell opened 9 months ago
0
Failed translation of Galaxy tool with ID containing a macro

#119 ddeepwell opened 9 months ago
0
Failed translation of Galaxy tool with output collections containing data with same name

#118 ddeepwell opened 9 months ago
0
messages, error handling, WDL ingest

#117 GraceAHall opened 11 months ago
0
Release v0.13.1

#116 rlupat closed 1 year ago
0
Documentation hotfixes

#115 GraceAHall closed 1 year ago
0
Janis pipelines workflows now translate.

#114 GraceAHall closed 1 year ago
0
all janis-pipelines workflows translating successfully

#113 GraceAHall closed 1 year ago
0
Release v0.13.0

#112 rlupat closed 1 year ago
0
Inplace workflow pruning

#111 GraceAHall closed 1 year ago
0
Redefine types in janis core

#110 GraceAHall closed 1 year ago
0
Release v0.12.0

#109 GraceAHall closed 1 year ago
1
Release v0.12.1

#108 rlupat closed 1 year ago
0
Added internals for ingestion as part of translation

#107 GraceAHall closed 1 year ago
1
ci: Fix Codecov upload and use new orb

#106 thomasrockhu-codecov closed 7 months ago
0
ModuleNotFoundError: No module named 'cwl_utils.parser_v1_2'

#105 ntachukwu opened 2 years ago
1
Re-enable test coverage

#104 kinow opened 3 years ago
2
Add exception handling to fromwdl

#103 illusional closed 3 years ago
0
Bump version for release

#102 illusional opened 3 years ago
0
Fix for no memory + memory expression

#101 illusional closed 3 years ago
2
Fix CWL stdout / stderr selection

#100 illusional opened 3 years ago
1
fromwdl: default memory value

#99 mr-c closed 3 years ago
0
fromwdl: allow cpus to refer to a WDL expression

#98 mr-c closed 3 years ago
1
fromwdl: missing optional inputs should result in empty conversion of WDL expressions, not half-empty strings with "null" inside

#97 mr-c opened 3 years ago
2
CWL generation: fix stdout

#96 mr-c closed 3 years ago
1
CWL generation: invalid result with output_type=File(), selector=Stdout() → "outputEval: _stderr"

#95 mr-c opened 3 years ago
1
fromwdl: Don't require runtime.disks

#94 mr-c closed 3 years ago
0
fromwdl: requires runtime.disks, yet that is optional in the spec

#93 mr-c closed 3 years ago
0
fromwdl: can't handle single character identifiers

#92 mr-c opened 3 years ago
1
Fix co-localisation of WDL secondary files

#91 illusional opened 3 years ago
3
convert to WDL: force co-localization of secondary_files

#90 mr-c opened 3 years ago
2
Avoid creating file in user desktop, fix typos and tests location

#89 kinow closed 3 years ago
0
Nextflow basic

#88 junyk closed 3 years ago
0
move variables used by input selectors to the top

#87 junyk closed 3 years ago
0
Release v0.12.0

#86 junyk closed 1 year ago
0
Nextflow: handle arguments of subworkflow within subworkflow

#85 junyk closed 3 years ago
0
Add runtime variables to python code tool process directive

#84 junyk closed 3 years ago
0
Nextflow: add runtime params as directives in nextflow process

#83 junyk closed 3 years ago
0
make sure ToolArgument select only the primary file

#82 junyk closed 3 years ago
0
Update import path

#81 junyk closed 3 years ago
0
Nextflow translations

#80 junyk closed 3 years ago
3
Release v0.11.4

#79 junyk closed 3 years ago
0
Add a preprocessor to find total size of an array of files

#78 xinzhel97 closed 3 years ago
0
use pytest to run unit tests

#77 junyk closed 3 years ago
0
Question: Is there a way to use your tool to convert WDL to CWL format

#76 michael-kotliar closed 3 years ago
4
Add a generic test for File data type

#75 xinzhel97 closed 3 years ago
1
Fix unittests

#74 junyk closed 3 years ago
0
Add minimal test to Tool class and array wrapper to Array class

#73 xinzhel97 closed 3 years ago
0
Allow TTestExpectedOutput to take generic parameters for preprocessors

#72 xinzhel97 closed 3 years ago
8