pypiper
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databio
Python toolkit for building restartable pipelines
When using a `Pipeline` and configuring the `outfolder` with a value that's _not_ an absolute path causes the `checkpoint` call to fail due to trying to write to a file...
With #220 , any `Stage` will be able to be marked as `nofail`, allowing the `Pipeline` of which it's part to continue. Whenever the pipeline ultimately finishes (or is halted...
With a `nofail`ed `Stage` now not writing a checkpoint (correct, IMO), `Stage`s downstream will be run even if they've already been done. Typically, I'll be marking a stage as `nofail`...
I just found 2 critical bugs with pypiper result reporting. Actually it may just be 2 outcomes from the same critical bug. When you report a result *it doesn't overwrite...
For a pipeline that uses `Stage`s, what about adding a `.describe()` method? If given no arguments, it could operate on all the pipeline's stages. Or it could take the name...
Reproduce by setting the multi flag to false or just leaving it out: ``` def test_temp_test(): pp = pypiper.PipelineManager( "sample_pipeline", outfolder="/home/drc/Downloads/BED_CLASSIFIER_OUTPUT/", multi=True ) ``` If you set the flag `multi=True`,...
After running tests locally, with `git status` I see... ```shell ... Untracked files: (use "git add ..." to include in what will be committed) tests/Data/pipeline_output/ tests/Data/pipeline_output3/ no changes added to...
From consideration of #210 , it becomes apparent that a user could specify a path to a logfile for a pipeline manager's logger to write to that would collide with...
Are the docs outdated? There are docs here: https://pep.databio.org/pypiper/report/ https://pep.databio.org/pypiper/pipestat/ and here that say: > Starting with pypiper v0.13.0 [pipestat](http://pipestat.databio.org/) is the recommended way of reporting pipeline statistics. But is...
When I'm trying to switch from a normal pypiper pipeline to one that configures pipestat, I'm getting this error: ``` Traceback (most recent call last): File "/home/nsheff/code/seqcolapi/analysis/pipeline/add_to_seqcol_server.py", line 92, in...