Added support for kraken2 #75
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Added support for kraken2. Multiple libraries are supported for minimap2 as well.
Pull Request Test Coverage Report for Build 2198481599Warning: 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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💛 - Coveralls |
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Thank you @charles-cowart, looks good, a few question and I think we are missing a test for when the minimap2 command has more than 2 references, no? ... The test can be a direct call to _gen_chained_cmd, just to make sure that they are generated fine and we don't mess something up with future changes.
| f' sr -t {self.nprocs} {self.mmi_db_path} - -a | ' | ||
| f'{self.samtools_path} fastq -@ {self.nprocs} -f 12 -F ' | ||
| f'256 -1 {path1} -2 {path2}') | ||
| result += (f' -l 100 -i {read1_input_path} -I {read2_input_path} -w ' |
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@charles-cowar, could you open an issue to define the min length of the reads via the config file or somewhere else that is not hardcoded? Thank you.
| print("LAST LINE EXPECTED ##################") | ||
| print(config['last_line']) | ||
| print("##################") | ||
| print("LAST LINE: %s" % lines_obs[-1]) |
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I think is fine to also remove the last print, no?
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definitely. done!
Added unittest for performing multiple minimap2 passes and kraken2.
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@antgonza unitest created for supplying multiple databases to minimap2 and kraken2 |
Added support for kraken2. Multiple libraries are supported for minimap2 as well.