diff --git a/README.md b/README.md index fa81f6935..1772c21f2 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 2023_03 + > git checkout 2023_06 > git submodule update --recursive --init Depending on your operating system, building instructions vary slightly: @@ -176,12 +176,20 @@ Changes of master since last release: * none so far -Changes in release 2023_03: +Changes in release 2023_06: -* NGSDImportEnsembl: Update to support Ensembl 109 -* RnaQC: Added target region to support targeted transcriptomics experiments +* new tools: GenesToTranscripts, NGSDImportSampleQC, GenesToTranscripts, TranscriptsToBed, NGSDExportGff. +* BamToFastq: Added support for single-end. +* MappingQC: Added support for read QC. +* VcfToBedpe: Added support for Sniffles, cuteSV and dipdiff. +* FastqExtract: Added parameter 'long_read'. +* ReadQC: Added parameter 'long_read'. +* NGSDExportSamples: added parameters 'run_after' and 'no_normal'. +* NGSDExportAnnotationData: speed-up by parallelization. * NGSD - * Added `ncbi_id` to `gene` table - * Added `folder_override`to `processed_sample` table + * Added 'side' enum to 'sequencing_run' table + * Added 'germline_mosaic' to 'variant' table + * Added 'hpo_obsolete' table with obsolete HPO terms + * Refactoring of 'expression' and 'gene_expression' tables to speed-up queries For older changes see [releases](https://github.com/imgag/ngs-bits/releases). diff --git a/doc/tools/NGSDExportGff.md b/doc/tools/NGSDExportGff.md index ecff56270..3c8c7f800 100644 --- a/doc/tools/NGSDExportGff.md +++ b/doc/tools/NGSDExportGff.md @@ -1,10 +1,10 @@ ### NGSDExportGff tool help - NGSDExportGff (2023_03-107-g2a1d2478) + NGSDExportGff (2023_03-106-gdd541c02) Writes all transcripts and exons of all genes to a gff3 file. Mandatory parameters: - -out The output file directory. + -out The output GFF file. Optional parameters: -test Uses the test database instead of on the production database. @@ -17,6 +17,6 @@ --tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'. ### NGSDExportGff changelog - NGSDExportGff 2023_03-107-g2a1d2478 + NGSDExportGff 2023_03-106-gdd541c02 [back to ngs-bits](https://github.com/imgag/ngs-bits) \ No newline at end of file diff --git a/src/NGSDExportGff/main.cpp b/src/NGSDExportGff/main.cpp index 5f4f06fb6..0802c2652 100644 --- a/src/NGSDExportGff/main.cpp +++ b/src/NGSDExportGff/main.cpp @@ -18,7 +18,7 @@ class ConcreteTool virtual void setup() { setDescription("Writes all transcripts and exons of all genes to a gff3 file."); - addOutfile("out", "The output file directory.", false); + addOutfile("out", "The output GFF file.", false); addFlag("test", "Uses the test database instead of on the production database."); }