Refactor module #25
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Refactor module #25
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… This is to avoid dir collisions with other repos
rehamFatima
reviewed
Jul 10, 2018
docs/adr.rst
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| 2018-06-27 - Remove reads marked as duplicate by BioBamBam | ||
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| BioBamBam only marks reads as duplicate, but does not remove the after. The Tool has been updated to remove the flagged duplicates using samtools with the parameter `-F 1024`. This matches the pipeline used within the `Blueprints project <http://dcc.blueprint-epigenome.eu/#/md/chip_seq_grch37>`_. |
docs/adr.rst
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| 2018-07-05 - Refactoring of repo to avoid naming collisions | ||
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| The original repo had the tools and tests in a directory that was in the root of the repo. This is problematic when there is sharing of the code as there are collisions in teh name space. This has meant that all of the code needs to be moved into a new subdirectory (mg_process_fastq). |
| [pytest] | ||
| #testpaths = tests | ||
| #testpaths = mg_process_fastq/tests | ||
| norecursedirs = data tmp* env docs apps basic_modules *.egg_info TADbit-master |
…tools to allow for easy importing into other pipelines.
…r moving this to the workflow.rst file
…efactored arrangement
…ce code duplication and allow for this script to be used as a single as part of the mg-tool-api
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Code refactoring to avoid namespace collisions when there are multiple repos that have used the same template