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Expose the functionality to suppress the creation of non-executable CWL and snakemake files. - #104
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…WL and snakemake files.
…generated. Also, check during ZIP creation whether the files do exist and ignore them, if not.
| // Write solutions (as CWL and Snakemake files and figures) to the file system. | ||
| APE.writeCWLWorkflows(candidateSolutions, true); | ||
| APE.writeSnakemakeWorkflows(candidateSolutions, true); | ||
| APE.writeCWLWorkflows(candidateSolutions, createPartialScripts); |
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Totally unrelated, but I just looked up the original implementation and made an issue as this might be redundant to define as such. Workflomics/ape#158
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Set myself as assignee, can refactor this.
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| runConfig.setSolutionPath(solutionPath); | ||
| int maxSol = runConfig.getMaxNoSolutions(); | ||
| runConfig.setNoCWL(maxSol); |
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It would be even better if Workflomics would provide these in the configJson, but not crucial atm
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You mean that APERunConfig sets the count of CWL/SMK/Graphs based on what is written in the configJson or that configJson contains an attribute for count of CWL/SMK/Graphs?
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Aah, I get it, @vedran-kasalica. You mean that workflomics-frontend sets the existing fields number_of_generated_graphs and number_of_cwl_files in configJson and RestAPE just collects the info from there. I will open an issue.
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Changes look good, I left a few comments, but it can be merged as it is.
Thanks for your review, will merge for now and work on the new issues as soon as I have some time. |
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Pull Request Overview
This PR uses the functionality from the APE backend to exclude "partial" scripts creation. If provided by the frontend,
the option
create_partial_scriptsis used by RestAPE and generation of CWL and Snakemake files for which the tool annotations are lacking the instructions/code to execute is skipped, ifcreate_partial_scriptsis set to false.Related Issue
None.
Changes Introduced
How Has This Been Tested?
Checklist