Merge pull request #874 from wtsi-npg/devel

pull from devel to master to create release 72.2.0

Changes

@@ -1,5 +1,17 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+release 72.2.0 (2024-08-30)
+ - npg_qc::autoqc::check::review:
+   1. To enable access to information about a sequencing run (from RunInfo.xml,
+      {r,R}unParameters.xml), added an optional 'runfolder_path' attribute.
+      The attribute will have to be set by the caller.
+   2. Added a new applicability criteria type - 'sequencing_run'
+   3. To avoid running the review check unnecessarily in the pipeline context,
+      moved ROBO criteria validation to the can_run method.
+   4. Introduced an option of defining the ROBO section within the default
+      section of the product configuration file.
+ - Explained QC outcome change for complex products (merged)
+
 release 72.1.2 (2024-08-05)
  - handle cases where the same tag sequence is seen in both index reads
 

MANIFEST

@@ -522,6 +522,9 @@ t/data/autoqc/review/not_hash/product_release.yml
 t/data/autoqc/review/mqc_type/product_release.yml
 t/data/autoqc/review/unknown_qc_type/product_release.yml
 t/data/autoqc/review/uqc_type/product_release.yml
+t/data/autoqc/review/default_and_study_section/product_release.yml
+t/data/autoqc/review/default_section/product_release.yml
+t/data/autoqc/review/wrong_default_and_study_section/product_release.yml
 t/data/autoqc/review/samplesheet_27483.csv
 t/data/autoqc/review/samplesheet_29524.csv
 t/data/autoqc/review/29524#2.composition.json
@@ -697,6 +700,7 @@ t/data/autoqc/200114_HS40_32710_A_H72VGBCX3/RunInfo.xml
 t/data/autoqc/200114_HS40_32710_A_H72VGBCX3/runParameters.xml
 t/data/autoqc/200114_HS40_32710_A_H72VGBCX3/InterOp/TileMetricsOut.bin
 t/data/autoqc/191210_MS2_MiSeq_walk-up_246_A_MS8539685-050V2/InterOp/TileMetricsOut.bin
+t/data/autoqc/191210_MS2_MiSeq_walk-up_246_A_MS8539685-050V2/RunParameters.xml
 t/data/autoqc/191210_MS2_MiSeq_walk-up_246_A_MS8539685-050V2/RunInfo.xml
 t/data/autoqc/200117_A00715_0080_BHY7T3DSXX/InterOp/TileMetricsOut.bin
 t/data/autoqc/200117_A00715_0080_BHY7T3DSXX/InterOp/ExtendedTileMetricsOut.bin

docs/qc_outcomes_change_howto.md

@@ -5,6 +5,48 @@
 - Wrap database changes into a transaction, which initially should have
   a clause to fail it so that it can be tried out (see some examples below).
 
+All listed below procedures were originally written for products containing
+one component. Existing procedures for changing the already existing QC outcomes
+should also work for products containing multiple components as long as these
+components are from the same run and are for the same tag index. Use any lane
+number (position) that went into the merged product. For example, for a product
+described by JSON below
+
+```json
+{
+  "__CLASS__": "npg_tracking::glossary::composition-101.3.0",
+  "components": [
+    {
+      "__CLASS__": "npg_tracking::glossary::composition::component::illumina-101.3.0",
+      "id_run": 49404,
+      "position": 7,
+      "tag_index": 1
+    },
+    {
+      "__CLASS__": "npg_tracking::glossary::composition::component::illumina-101.3.0",
+      "id_run": 49404,
+      "position": 8,
+      "tag_index": 1
+    }
+  ]
+}
+```
+
+use the following expression for a search when toggling the QC outcome
+
+```
+my $rs=npg_qc::Schema->connect()->resultset("MqcLibraryOutcomeEnt")
+  ->search_autoqc({id_run=>49494,position=>7,tag_index=>1});
+```
+
+The custom `search_autoqc` method returns a resultset containing QC outcomes for
+products which contain a component with position 7 and tag_index 1, which will
+be the merged product described by the above JSON. If the QC database records
+are correct, the resultset should contain one row. The same resultset is
+returned if 8 is used as the value of the position. There should not be any need
+to repeat the process for every position that went into the merge and in a case
+of a toggle this would be wrong.
+
 ## Toggle the outcome of a single library
 
 QC outcome will change from `pass` to `fail` or `fail` to `pass`.