update docu for release 2024_08

README.md

@@ -15,7 +15,7 @@ Alternatively, *ngs-bits* can be built from sources. Use git to clone the most r
 
     > git clone --recursive https://github.com/imgag/ngs-bits.git
 	> cd ngs-bits
-	> git checkout 2024_07
+	> git checkout 2024_08
 	> git submodule update --recursive --init
 
 Depending on your operating system, building instructions vary slightly:
@@ -177,15 +177,13 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 
 ## ChangeLog
 
-Changes in release 2024_07:
+Changes in release 2024_08:
 
-* BedCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter `-random_access`)
-* BedHighCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter `-random_access`)
-* BedLowCoverage: improved runtime by using chromosomal sweep instead of random access (added parameter `-random_access`)
-* VcfAnnotateConsequence: added support for RefSeq GFF file
-* VcfFilter: added parameter `-filter_clear`
-* NGSD:
-	* kasp_status: added fields `calculated_date` and `calculated_by`.
+* added tool: CnvReferenceCohort
+* removed tool: NGSDMaintain (functionality now in GSvar NGSD maintainance dialog)
+* NGSDExportSamples: added option `-add_study_column`
+* NGSDSameSample: added option `-include_bad`
+* NGSD: added new table `runqc_ont`
 
 
 

doc/tools/NGSDExportSamples.md

@@ -1,5 +1,5 @@
 ### NGSDExportSamples tool help
-	NGSDExportSamples (2024_02-42-g36bb2635)
+	NGSDExportSamples (2024_07-35-gb854a4ba)
 
 	Lists processed samples from the NGSD.
 
@@ -81,6 +81,8 @@
 	                             Default value: 'false'
 	  -add_lab_columns           Adds columns input, molarity, operator, processing method and batch number.
 	                             Default value: 'false'
+	  -add_study_column          Add a column with studies of the sample.
+	                             Default value: 'false'
 	  -test                      Uses the test database instead of on the production database.
 	                             Default value: 'false'
 
@@ -91,8 +93,11 @@
 	  --tdx                      Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDExportSamples changelog
-	NGSDExportSamples 2024_02-42-g36bb2635
+	NGSDExportSamples 2024_07-35-gb854a4ba
 
+	2024-08-21 Added 'add_study_column' flag.
+	2024-04-24 Added 'only_with_small_variants' flag.
+	2024-03-04 Added 'add_lab_columns' flag.
 	2023-11-16 Added 'add_call_details' flag.
 	2023-07-13 Added 'add_dates' flag.
 	2022-11-11 Added 'ancestry' and 'phenotypes' filter options.

doc/tools/NGSDSameSample.md

@@ -1,5 +1,5 @@
 ### NGSDSameSample tool help
-	NGSDSameSample (2023_11-42-ga9d1687d)
+	NGSDSameSample (2024_07-35-gb854a4ba)
 
 	For the given processed sample, lists all processed samples of the same patient or sample.
 
@@ -20,7 +20,9 @@
 	  -mode <enum>          Type of relation (either only same-sample or same-patient (includes same-sample).
 	                        Default value: 'SAME_PATIENT'
 	                        Valid: 'SAME_SAMPLE,SAME_PATIENT'
-	  -include_merged       Include merged samples in the output (will be ignored on default).
+	  -include_bad          Include bad processed samples in the output (will be ignored on default).
+	                        Default value: 'false'
+	  -include_merged       Include merged quality processed samples in the output (will be ignored on default).
 	                        Default value: 'false'
 	  -test                 Uses the test database instead of on the production database.
 	                        Default value: 'false'
@@ -32,8 +34,9 @@
 	  --tdx                 Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDSameSample changelog
-	NGSDSameSample 2023_11-42-ga9d1687d
+	NGSDSameSample 2024_07-35-gb854a4ba
 
-	2023-11-21 remove merged sample on default
+	2024-08-22 remove bad samples by default
+	2023-11-21 remove merged samples by default
 	2023-11-15 initial commit
 [back to ngs-bits](https://github.com/imgag/ngs-bits)