Qc check rnaseqc #392
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Qc check rnaseqc #392
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added 30 commits
August 10, 2015 14:37
Conflicts: .gitignore
- Done some code reformatting
- Use npg_qc::autoqc::results::collection instead to iterate through a list of available results
…Readonly::Array - Move all POD at the end of module
- Update data/schema.txt: added new table to npg_qc database to store QC check: rna_seqc - New file: lib/npg_qc/Schema/Result/RnaSeqc.pm: added new object for storage using DBIx - Schema::Result::SeqComposition was updated with a new ER relationship - rna_seqc is no longer a non-storable qc check and does not have to be skiped by qc_store any more.
- Create new template file for RNA-SeQC check: npg_qc_viewer/root/src/ui_checks/rna_seqc.tt2 - about.tt2: Rearrange list of available checks alphabetically and - add rna_seqc to the list of available checks - about_qc_checks.tt2: rearrange information about qc checks alphabetically and - add "about" information for rna_seqc metrics
- Bug fix: mega bug in which the value of metrics were being rounded up because the type of the columns was integer instead of floating point. - Bug fix: Value of "End 2 % Sense" is not being stored because of a trailing \n (being the last column). Use chomp on keys to fix.
- rna_seqc check template shows nicely formatted results and includes a link to the qc/rna_seqc directory where all of the reports are stored - reorganize keys in hash of labels alphabetically in the summary table's template(what's wrong with that?) - add rna_seqc label and its 3 chosen metrics to said list - add selected rna_seqc metrics to summary table in lanes template - fix misspelled name for the Broad in info page
… anymore - New attribute allows schema object to play nice with qc_store new capabilities
…aseqc_with_mgcam_rpt4composition Conflicts: scripts/npgqc_dbix_schema_loader.pl
added 7 commits
December 5, 2016 14:52
- Reverse previous change that prevented rendering metrics for rna_seqc check because they was no rna_seqc template
- Link to RNA-SeQC report can be display only if id_run is defined, and this is true only when check results are being loaded from disk. - Metrics in summary table are shown in a single line to reduce scrolling.
- Travis complains about unexpected closing tags
[fixed] Conflicts: Changes
mgcam
reviewed
Dec 9, 2016
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| has [ @ATTRIBUTES ] => ( | ||
| is => 'rw', | ||
| isa => 'Maybe[Num]', |
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Would like to chat this particular case over. I think important here are
- reflecting what data we are capturing and
- consistency serializing to the DB.
mgcam
reviewed
Dec 9, 2016
| CREATE TABLE `rna_seqc` ( | ||
| `id_rna_seqc` bigint(20) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Auto-generated primary key', | ||
| `id_seq_composition` bigint(20) unsigned NOT NULL COMMENT 'A foreign key referencing the id_seq_composition column of the seq_composition table', | ||
| `path` varchar(256) DEFAULT NULL, |
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I am not sure that this field is going to be filled by this check. This is a historic feature, which we probably can discontinue.
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A file with an SQL statement that will update a database is needed in https://github.com/wtsi-npg/npg_qc/tree/devel/scripts/upgrade_schema |
added 2 commits
December 12, 2016 13:46
…pes where appropriate - Change data type of rna_seqc result attributes from Maybe[Num] to Num. - Update rna_seqc Schema to reflect removed column. - Add file upgrade_schema-60.x to create table rna_seqc. - Update Changes file
added 2 commits
January 5, 2017 17:18
Check: - Make attributes lazy+build instead of lazy_build - Add new attribute to create a directory by default into which RNA-SeQC's report will be stored (the directory itself is created by RNA-SeQC) - Fix the parsing code to reflect this change - Set to undef fields with value of NaN when parsing Result: - Add new output_dir directory to RNA-SeQC result object Tests: - Create subtests for categories of tests - Add tests for parsing the metrics file - Improve testing by adding more units - Add auxiliary files for testing
- Add missing auxiliary tests files
added 3 commits
January 18, 2017 14:37
…in npg_qc_viewer - This is to reflect the changes that happened in the check, i.e. the creation of the directory inside the archive/lane/qc directory by default.
- This is necessary for the npg_autoqc_data.pl script to work for this check.
ces
reviewed
Jan 19, 2017
| `end_3_norm` float unsigned DEFAULT NULL, | ||
| `other_metrics` text, | ||
| PRIMARY KEY (`id_rna_seqc`), | ||
| KEY `rna_seqc_compos` (`id_seq_composition`), |
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needs updating now - change to;
UNIQUE KEY rna_seqc_id_compos_unq (id_seq_composition),
- Modify SQL commands to reflect changes in rna_seqc table. - Update upgrade-schema-60.x SQL script as well as data/schema.txt. - Change rna_seqc check POD 'DESCRIPTION' to be more accurate. - Delete instances of the qc_report_dir attribute which is no longer used. - Update Changes file with latest er... changes.
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All changes are about RNA-SeQC template in SeQC. Requires rna_seqc table in npg_qc db (npgqctest_rb11 schema in npgtest-db can be used).