Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / scipipe/scipipe issues and pull requests

#160 - 159 combinator

Pull Request - State: open - Opened by samuell 6 months ago - 1 comment

#159 - Create a generic combinator component

Issue - State: open - Opened by samuell 6 months ago - 1 comment

#158 - Make FileIP handle multiple paths

Issue - State: open - Opened by samuell about 1 year ago

#157 - Add a `.fromPaths()` on in-ports.

Issue - State: closed - Opened by samuell about 1 year ago - 1 comment
Labels: enhancement

#156 - Add a `scipipe cleantemp` command to clean temporary folders

Issue - State: open - Opened by samuell about 1 year ago - 6 comments
Labels: enhancement, good first issue

#155 - Test suite leaves trailing temporary run directory

Issue - State: open - Opened by samuell over 1 year ago
Labels: bug

#154 - Broken example link

Issue - State: closed - Opened by apaleyes almost 2 years ago - 4 comments

#153 - Concatenator component is apparently not thread-safe

Issue - State: open - Opened by samuell almost 2 years ago - 1 comment
Labels: bug

#152 - Better functionality for producing combinations of file inputs and parameters

Issue - State: open - Opened by samuell about 2 years ago
Labels: enhancement

#151 - Idea for a flexible component to generate parameters dynamically from shell code

Issue - State: open - Opened by samuell over 2 years ago
Labels: enhancement

#150 - delete minor unreachable code caused by log.Fatal

Pull Request - State: closed - Opened by Abirdcfly over 2 years ago

#149 - Requests for a tool that monitors the execution of scipipe workflows.

Issue - State: open - Opened by zhangzhen over 2 years ago - 2 comments

#148 - Merge tags and params?

Issue - State: open - Opened by samuell over 2 years ago

#147 - Order globs on file size

Issue - State: open - Opened by jonalv almost 3 years ago

#146 - Fix unhandled errors (and add check in CI pipeline)

Issue - State: closed - Opened by samuell over 3 years ago
Labels: bug

#145 - Enable renaming paths to final paths on different partition

Issue - State: open - Opened by samuell over 3 years ago
Labels: enhancement

#144 - Ability to depend on task completion

Issue - State: open - Opened by samuell over 3 years ago
Labels: enhancement

#142 - Apparent TempDir collisions

Issue - State: closed - Opened by samuell over 3 years ago
Labels: bug

#141 - Update task.go

Pull Request - State: open - Opened by jonalv over 3 years ago - 1 comment

#140 - Use os.MkdirTemp() for temporary directories in tests

Issue - State: open - Opened by samuell over 3 years ago
Labels: enhancement

#139 - Remove duplicated Fail/Failf/Audit/Auditf functions

Issue - State: closed - Opened by samuell over 3 years ago
Labels: enhancement

#138 - Create a join component, to operate on tags

Issue - State: open - Opened by samuell over 3 years ago - 2 comments

#137 - Make sure that tags are are properly forwarded

Issue - State: open - Opened by samuell over 3 years ago

#134 - Make all errors log from Processes or Tasks, and include process/task name in output

Issue - State: closed - Opened by samuell over 3 years ago
Labels: enhancement

#133 - Investigate effects of increasing channel buffer size

Issue - State: open - Opened by samuell over 3 years ago

#131 - Runtime panic when trying to trim a larger piece than original string

Issue - State: closed - Opened by samuell over 3 years ago
Labels: bug

#130 - basename modifier should not prepend parent dir before path

Issue - State: closed - Opened by samuell over 3 years ago
Labels: bug

#129 - Add crossvalidation component from cheminformatics demo

Issue - State: open - Opened by jonalv over 3 years ago

#128 - More logging in the globber component

Issue - State: open - Opened by samuell over 3 years ago
Labels: enhancement, good first issue

#127 - Concatenator component should create a merged audit file

Issue - State: open - Opened by samuell almost 4 years ago - 1 comment
Labels: bug

#126 - Add method for easily adding inline scipts

Issue - State: open - Opened by samuell almost 4 years ago
Labels: enhancement

#124 - Add shorter methods for creating shell and func-processes, with auto-generated names.

Issue - State: open - Opened by samuell almost 4 years ago
Labels: enhancement

#123 - Allow specifying output path formats inline in the command pattern

Issue - State: open - Opened by samuell almost 4 years ago
Labels: enhancement

#122 - Add a synchronous IP Selector component

Pull Request - State: closed - Opened by samuell almost 4 years ago - 2 comments

#121 - Include stack traces for error messages

Issue - State: open - Opened by samuell almost 4 years ago - 1 comment
Labels: enhancement

#120 - Output paths with ../ are not contained in the temporary execution folder

Issue - State: closed - Opened by samuell almost 4 years ago
Labels: bug

#119 - Add component for flexibly filtering inputs

Issue - State: closed - Opened by samuell almost 4 years ago
Labels: enhancement

#118 - Add easy way to tag all outputs from a process

Issue - State: open - Opened by samuell almost 4 years ago
Labels: enhancement

#117 - PlotGraphPDF can not write to directory that does not exist

Issue - State: closed - Opened by jonalv almost 4 years ago
Labels: bug, good first issue

#116 - Fix #111: Make channel buffert size configurable via environment variable

Pull Request - State: closed - Opened by samuell almost 4 years ago - 1 comment

#115 - Serialized workflow description in JSON ?

Issue - State: closed - Opened by nyue almost 4 years ago - 2 comments
Labels: question

#114 - Document how contribution can be performed.

Pull Request - State: closed - Opened by nyue almost 4 years ago - 1 comment

#113 - Contributing to scipipe - working with github+golang

Issue - State: closed - Opened by nyue almost 4 years ago - 4 comments

#112 - Implement dirname

Pull Request - State: closed - Opened by szliao over 4 years ago - 2 comments

#111 - Provide functionality for defining buffer size

Issue - State: closed - Opened by jonalv over 4 years ago
Labels: enhancement

#110 - Cloud execution

Issue - State: closed - Opened by multimeric over 4 years ago - 3 comments
Labels: enhancement

#109 - Enable Concatenator to group output by tag

Issue - State: closed - Opened by samuell over 4 years ago - 1 comment
Labels: enhancement

#108 - components.NewConcatenator swallows newlines

Issue - State: closed - Opened by jonalv over 4 years ago
Labels: bug

#107 - Implement a `dirname` modifier for paths.

Issue - State: closed - Opened by samuell over 4 years ago
Labels: good first issue

#106 - FIFO files are created in temporary folder not working dir

Issue - State: closed - Opened by samuell over 4 years ago

#103 - fromPath on ports

Issue - State: open - Opened by jonalv over 4 years ago - 1 comment
Labels: enhancement

#102 - Allow taking a static parameter as string in parameter placeholder

Issue - State: open - Opened by samuell over 4 years ago
Labels: enhancement

#101 - SciPipe doesn't fail on missing output files

Issue - State: closed - Opened by samuell over 4 years ago - 2 comments
Labels: bug

#100 - Handle differently sized input on ports by repeating the chunk in the process

Issue - State: open - Opened by jonalv over 4 years ago - 1 comment
Labels: enhancement

#98 - Update resequencing.go

Pull Request - State: closed - Opened by dahlo over 4 years ago - 2 comments

#97 - fixed name

Pull Request - State: closed - Opened by jonalv over 4 years ago - 2 comments

#96 - Add support for go modules

Pull Request - State: closed - Opened by dwmunster almost 5 years ago

#95 - Graph plotting is incomplete for some workflows.

Issue - State: closed - Opened by samuell almost 5 years ago - 1 comment
Labels: bug, invalid

#94 - Potential Seg Fault in Task.AtomizeIPs

Issue - State: open - Opened by dwmunster almost 5 years ago - 2 comments
Labels: bug

#93 - Formatting error in audit2bash

Issue - State: closed - Opened by samuell about 5 years ago

#92 - Fix #71

Pull Request - State: closed - Opened by kerkomen over 5 years ago - 2 comments

#91 - Resolve the StreamToSubstream function failing to pass the checkFilename() validation

Pull Request - State: closed - Opened by rbisewski over 5 years ago - 1 comment

#90 - fix small typo

Pull Request - State: closed - Opened by JakeHagen over 5 years ago

#89 - Hash SubStream IP Paths for TempDir

Pull Request - State: closed - Opened by dwmunster over 5 years ago

#88 - [WIP] Windows Compatibility Fixes

Pull Request - State: open - Opened by dwmunster over 5 years ago - 8 comments

#87 - Add test for AtomizeIPs' extra file moving

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 1 comment

#86 - Tests do not pass on Windows

Issue - State: open - Opened by dwmunster over 5 years ago
Labels: bug, good first issue

#85 - Fix issue with overwriting tags.

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 4 comments

#84 - Add Appveyor Testing for Windows

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 1 comment

#83 - Add select based Task processing.

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 1 comment

#82 - Use Channels to Handle Task Order

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 1 comment

#81 - Deadlocks When >16 Tasks Are Needed With Multiple Downstream Receivers

Issue - State: closed - Opened by dwmunster over 5 years ago - 1 comment
Labels: bug

#80 - Add ParamCombinator Component

Pull Request - State: closed - Opened by dwmunster over 5 years ago

#79 - Change TempDir to Use a Hash of Task Information for the Directory Name.

Pull Request - State: closed - Opened by dwmunster over 5 years ago - 2 comments

#78 - Filename "" does not match expression [A-Za-z\/\.-_]+

Issue - State: closed - Opened by JakeHagen over 5 years ago - 4 comments
Labels: bug

#77 - Procs Without Outputs May Cause Deadlocks

Issue - State: closed - Opened by dwmunster over 5 years ago - 2 comments
Labels: bug

#76 - Respect return codes, not just stderr output, to trigger error

Issue - State: closed - Opened by samuell over 5 years ago - 1 comment
Labels: bug

#75 - make temp working directory removable

Issue - State: open - Opened by paul-asvb almost 6 years ago - 2 comments
Labels: enhancement

#74 - Suggestion for #72

Pull Request - State: closed - Opened by paul-asvb almost 6 years ago - 7 comments

#73 - make path for log files configurable

Issue - State: open - Opened by paul-asvb almost 6 years ago - 5 comments
Labels: enhancement

#72 - Add variable for the concrete path of the temporary task run dir in shell command pattern

Issue - State: open - Opened by samuell almost 6 years ago
Labels: enhancement

#71 - Can not run a workflow with a single process

Issue - State: closed - Opened by samuell almost 6 years ago
Labels: bug

#70 - Can not use a variable in an absolute path

Issue - State: closed - Opened by PaschalisAthan about 6 years ago - 5 comments
Labels: help wanted

#69 - Generate commands with a Go func

Issue - State: open - Opened by samuell over 6 years ago
Labels: enhancement

#68 - Update CI config to CircleCI 2.0

Issue - State: closed - Opened by samuell over 6 years ago - 1 comment

#67 - Separate logs should be kept and written per workflow

Issue - State: open - Opened by samuell over 6 years ago
Labels: enhancement

#66 - In- and out-ports with the same name can't co-exist

Issue - State: closed - Opened by samuell over 6 years ago - 2 comments
Labels: bug

#62 - Rename AuditInfo.Keys to AuditInfo.Tags

Issue - State: closed - Opened by samuell over 6 years ago - 1 comment
Labels: enhancement

#59 - Why Go?

Issue - State: closed - Opened by rizplate over 6 years ago - 6 comments
Labels: question

#58 - Add workflow graph visualization

Issue - State: closed - Opened by samuell over 6 years ago - 1 comment

#57 - Create default path configuration

Issue - State: closed - Opened by samuell over 6 years ago - 1 comment
Labels: enhancement

#56 - Update docs about removed ExpandParams method

Issue - State: closed - Opened by samuell over 6 years ago - 1 comment