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Record all recent changes #773

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merged 2 commits into from
Oct 31, 2023
Merged

Record all recent changes #773

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Record all recent changes
mgcam Oct 31, 2023
1035236
Fixed typos and deleted superfluous commas
mgcam Oct 31, 2023
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LIST OF CHANGES

- Removed the use of 'xml' lims driver from all tests.
- Deleted 'xml' lims driver class and all classes, which supported this
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Suggested change
- Deleted 'xml' lims driver class and all classes, which supported this
- Deleted 'xml' lims driver class and all classes which supported this

functionality, together with all related tests and test data.
- In release 97.0.0, ihe default LIMS driver type in samplesheet generation
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Suggested change
- In release 97.0.0, ihe default LIMS driver type in samplesheet generation
- In release 97.0.0, the default LIMS driver type in samplesheet generation

was changed to 'ml_warehouse'. Following this change, the code for
auto-generation of MiSeq default samplesheets is now simplified to exclude
an explicit creation of LIMS objects.
- Changes to st::api::lims, which are not related to the 'xml' lims driver
removal:
- deleted all previously deprecated methods ('seq_qc_state',
'associated_lims', 'associated_child_lims', 'associated_child_lims_ia');
- deleted methods, for which we do not have data in ml warehouse, our
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- deleted methods, for which we do not have data in ml warehouse, our
- deleted methods for which we do not have data in ml warehouse, our

primary source of LIMS data ('request_id', 'project_id', 'project_name');
- deleted all code for computing inline tag indexes and inferring
tag sequences and library types from sample description since
definitions like this have not been in use for the last six years;
- reimplemented the 'reference_genome' method to exclude a fallback to
a study reference for tag zero and lane-level objects when samples
have different references.
- Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to
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Suggested change
- Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to
- Restricted the 'all_lanes_mergeable' flag in the 'long_info' role to

NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run
since HiSeq instruments are no longer used.
- Updated DBIx classes from the prod database. Changes are due to the MySQL
database server upgrade to v8.+
- Finding the runfolder path - stopped errors being raised when a runfolder
is found in 'analysis' or 'outgoing' in the presence of a duplicate runfolder
in 'incoming' (the duplicates in 'incoming' are sometimes created by
instruments well after the run was mirrored and the runfolder moved to
'analysis'). The duplicate runfolder in 'incoming' is disregarded'.

release 97.0.0
- Change CI workflow to standard file name
- Change to Perl versions from Perlbrew
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