From b451c5eeef46fe6e1d42e1f434187c9aed50d4a0 Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Tue, 27 Aug 2024 08:19:21 +0200 Subject: [PATCH] update docu for release 2024_08 --- README.md | 16 +++++++--------- doc/tools/NGSDExportSamples.md | 9 +++++++-- doc/tools/NGSDMaintain.md | 23 ----------------------- doc/tools/NGSDSameSample.md | 11 +++++++---- 4 files changed, 21 insertions(+), 38 deletions(-) delete mode 100644 doc/tools/NGSDMaintain.md diff --git a/README.md b/README.md index e1257f612..6c0b95f12 100644 --- a/README.md +++ b/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` diff --git a/doc/tools/NGSDExportSamples.md b/doc/tools/NGSDExportSamples.md index c8b6110a7..0cd89e49f 100644 --- a/doc/tools/NGSDExportSamples.md +++ b/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. diff --git a/doc/tools/NGSDMaintain.md b/doc/tools/NGSDMaintain.md deleted file mode 100644 index b29e4619b..000000000 --- a/doc/tools/NGSDMaintain.md +++ /dev/null @@ -1,23 +0,0 @@ -### NGSDMaintain tool help - NGSDMaintain (2018_11-7-g60f117b) - - Checks for and corrects errors/inconstistencies in the NGSD database. - - Optional parameters: - -out Output file. If unset, writes to STDOUT. - Default value: '' - -fix Correct found errors/inconstistencies. - Default value: 'false' - -test Uses the test database instead of on the production database. - Default value: 'false' - - Special parameters: - --help Shows this help and exits. - --version Prints version and exits. - --changelog Prints changeloge and exits. - --tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'. - -### NGSDMaintain changelog - NGSDMaintain 2018_11-7-g60f117b - -[back to ngs-bits](https://github.com/imgag/ngs-bits) \ No newline at end of file diff --git a/doc/tools/NGSDSameSample.md b/doc/tools/NGSDSameSample.md index cc7b106c5..86c36ce7a 100644 --- a/doc/tools/NGSDSameSample.md +++ b/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 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) \ No newline at end of file