ConvertJob.copy_sequences() method added. #145
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Method allows caller to copy the fastq files associated w/a sample-name and a project into another project.
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Will add Amanda to the project as well. |
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charles-cowart
changed the title
Pull Request Test Coverage Report for Build 9912490051Warning: This coverage report may be inaccurate.This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.
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@antgonza Ready for review! |
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Hi @AmandaBirmingham ! The functionality is now ready. Would you mind reviewing? Thank you! |
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Just a couple of things. I can re-review once @AmandaBirmingham changes are implemented.
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Ready for review! I did a little bit of interpretation with @AmandaBirmingham 's last suggestion. Please let me know what you guys think. |
copy_sequences() will now copy all replicates if a sample contains replicates. Copying a single replicate is no longer an option.
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@AmandaBirmingham @antgonza ready for review! |
| @@ -146,6 +151,9 @@ def run(self, callback=None): | |||
| job_info = self.submit_job(self.job_script_path, | |||
| exec_from=self.log_path, | |||
| callback=callback) | |||
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| self._get_sample_sheet_info() | |||
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Just to confirm, can this be called before the previous line or not (before submitting jobs)? Also, is the plan to unify this functionality in a single place? Maybe _get_sample_sheet_info()?
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This function should only be called after the bcl-convert job returns completed. The output from this method is specific to supporting ConvertJob so there currently isn't a value in pushing it down into the base class. It's name does begin with '_' and so by convention it's an internal method and nobody should be calling it except ConvertJob.run().
Method allows caller to copy the fastq files associated w/a sample-name and a project into another project.
Needs unit-tests.