diff --git a/HISTORY.md b/HISTORY.md index d36883d37..e5090eed1 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,8 +1,9 @@ -## 1.1.0 (in progress) +## 1.1.0 (11 July 2018) -- Unzip GTF file prior to installation when installing a custom genome. - Germline calls: rename outputs to `samplename-germline` to provide easier to understand outputs in final directory. +- Add bcbioRNASeq object creation and automatic quality report generation + with `tools_on: [bcbiornaseq]` - CWL: Support germline/somatic calling for tumor samples. - CNVkit: improve whole genome runs. Better speed in normalize_sv_coverage through parallelization and avoiding logging. Avoid memory errors in segmentation. @@ -17,6 +18,7 @@ - CWL: adjust defaults for align_split_size and nomap_split_targets to match different parallelization and overhead for these runs - CWL: support for Cromwell runner +- custom genomes: Unzip GTF file prior to installation. - Avoid making variant_regions required during processing (by filling with coverage) to differentiate targeted and non analyses downstream. - Avoid attempts to download pre-installed S3 genomes, providing better @@ -31,7 +33,6 @@ - Adding BAM file for each sample in small-RNAseq pipeline, samtools and qualimap qc metrics to multiqc report. - Allow arbitrary genomes for ChIP-seq. Thanks to @evchambers for pointing out the issue. -- Add bcbioRNASeq object creation and automatic quality report generation. ## 1.0.9 (10 April 2018) diff --git a/docs/conf.py b/docs/conf.py index 92a1da79d..91a8fb23f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -48,9 +48,9 @@ # built documents. # # The short X.Y version. -version = '1.0.9' +version = '1.1.0' # The full version, including alpha/beta/rc tags. -release = '1.0.9' +release = '1.1.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/requirements-conda.txt b/requirements-conda.txt index 5b5651f8d..ad982b616 100644 --- a/requirements-conda.txt +++ b/requirements-conda.txt @@ -1 +1 @@ -bcbio-nextgen=1.0.9 +bcbio-nextgen=1.1.0 diff --git a/requirements.txt b/requirements.txt index b6b03259f..c16b8ff53 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1 +1 @@ -bcbio-nextgen==1.0.9 +bcbio-nextgen==1.1.0 diff --git a/setup.py b/setup.py index 1a8ba1118..6b70eccbe 100755 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ import os from setuptools import setup, find_packages -version = "1.1.0a0" +version = "1.1.0" def write_version_py(): version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline',