Mercurial > repos > kls286 > chap_test_20230328
comparison README.md @ 4:649eb2ea2f49 draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0
| author | kls286 |
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| date | Tue, 28 Mar 2023 15:37:28 +0000 |
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| 3:1cf636a22185 | 4:649eb2ea2f49 |
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| 1 ### Pipeline | |
| 2 This package conains proof of concepts pipeline framework for workflow | |
| 3 execution. It requires proper configuration of pipeline in terms classes, e.g. | |
| 4 ``` | |
| 5 # pipeline deifinition as sequence of objects | |
| 6 pipeline: | |
| 7 - reader.Reader | |
| 8 - processor.Processor | |
| 9 - fitter.Fitter | |
| 10 - processor.Processor | |
| 11 - writer.Writer | |
| 12 - fitter.Fitter | |
| 13 - writer.Writer | |
| 14 | |
| 15 # specific object parameters, e.g. our reader accepts fileName=data.csv | |
| 16 reader.Reader: | |
| 17 fileName: data.csv | |
| 18 | |
| 19 | |
| 20 # specific object parameters, e.g. our writer accepts fileName=data.out | |
| 21 writer.Writer: | |
| 22 fileName: data.out | |
| 23 ``` | |
| 24 | |
| 25 Then, you may execute this pipeline as following: | |
| 26 ``` | |
| 27 ./runner.py --config config.yaml | |
| 28 ``` | |
| 29 and, check the output in `data.out` file. | |
| 30 |