diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 012f80c88..4dbb30f91 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,9 +11,10 @@ Added: * SVdb to the varcall_py36 container #871 * SVdb to WGS workflow #871 * Docker container for vcf2cytosure #858 -* Snakemake rule for creating `.cgh` files from `CNVkit` outputs #858 -* SVdb to TGA workflow #871 +* Snakemake rule for creating `.cgh` files from `CNVkit` outputs #858 +* SVdb to TGA workflow #871 * SVdb merge SV and CNV #871 +* QC-only workflow #847 Changed: ^^^^^^^^ @@ -41,7 +42,7 @@ Added: ^^^^^^ * Added the readthedocs page for BALSAMIC variant-calling filters #867 -* Project requirements (setup.py) to build the docs #874 +* Project requirements (setup.py) to build the docs #874 * Generate cram from umi-consensus called bam files #865 Changed: @@ -95,11 +96,11 @@ Added: Fixed: ^^^^^^ -* Add default for gender if ``purecn`` captures dual gender values #824 +* Add default for gender if ``purecn`` captures dual gender values #824 Changed: ^^^^^^^^ -* Updated ``purecn`` and its dependencies to latest versions +* Updated ``purecn`` and its dependencies to latest versions [8.2.2] ------- @@ -129,7 +130,7 @@ Added: * Added various basic filters to all variant callers irregardless of their delivery status #750 * BALSAMIC container #728 -* BALSAMIC reference generation via cluster submission for both reference and container #686 +* BALSAMIC reference generation via cluster submission for both reference and container #686 * Container specific tests #770 * BALSAMIC quality control metrics extraction and validation #754 * Delly is added as a submodule and removed from rest of the conda environments #787 @@ -167,12 +168,12 @@ Fixed: * Bumped version for ``bcftools`` in cnvkit container * Fixed issues #776 and #777 with correct install paths for gatk and manta * Fixed issue #782 for missing AF in the vcf INFO field -* Fixed issues #748 #749 with correct sample names +* Fixed issues #748 #749 with correct sample names * Fixed issue #767 for ascatngs hardcoded values -* Fixed missing output option in bcftools filters for tnhaplotyper #793 +* Fixed missing output option in bcftools filters for tnhaplotyper #793 * Fixed issue #795 with increasing resources for vep and filter SV prior to vep * Building ``wheel`` for ``cryptography`` bug inside BALSAMIC container #801 -* Fixed badget for docker container master and develop status +* Fixed badget for docker container master and develop status * ReadtheDocs building failure due to dependencies, fixed by locking versions #773 * Dev requirements installation for Sphinx docs (Github Action) #812 * Changed path for main Dockerfile version in ``.bumpversion.cfg`` @@ -186,7 +187,7 @@ Added: * Workflow to check PR tiltes to make easier to tell PR intents #724 * ``bcftools stats`` to calculate Ti/Tv for all post annotate germline and somatic calls #93 * Added reference download date to ``reference.json`` #726 -* ``ascatngs`` hg38 references to constants #683 +* ``ascatngs`` hg38 references to constants #683 * Added ClinVar as a source to download and to be annotated with VCFAnno #737 Changed: @@ -248,7 +249,7 @@ Added: * Individual rules (i.e. ngs filters) for cnv and sv callers. Only Manta will be delivered and added to the list of output files. #708 * Added "targeted" and "wgs" tags to variant callers to provide another layer of separation. #708 * ``manta`` convert inversion #709 -* Sentieon version to bioinformatic tool version parsing #685 +* Sentieon version to bioinformatic tool version parsing #685 * added ``CITATION.cff`` to cite BALSAMIC @@ -257,9 +258,9 @@ Changed: * Upgrade to latest sentieon version 202010.02 * New name ``MarkDuplicates`` to ``picard_markduplicates`` in ``bwa_mem`` rule and ``cluster.json`` -* New name rule ``GATK_contest`` to ``gatk_contest`` +* New name rule ``GATK_contest`` to ``gatk_contest`` * Avoid running pytest github actions workflow on ``docs/**`` and ``CHANGELOG.rst`` changes -* Updated ``snakemake`` to ``v6.5.3`` #501 +* Updated ``snakemake`` to ``v6.5.3`` #501 * Update ``GNOMAD`` URL * Split Tumor-only ``cnvkit batch`` into individual commands * Improved TMB calculation issue #51 @@ -277,7 +278,7 @@ Fixed: * post-processing of the umi consensus in handling BI tags * vcf-filtered-clinical tag files will have all variants including PASS * Refactor snakemake ``annotate`` rules according to snakemake etiquette #636 -* Refactor snakemake ``align`` rules according to snakemake etiquette #636 +* Refactor snakemake ``align`` rules according to snakemake etiquette #636 * Refactor snakemake ``fastqc`` ``vep`` contest and ``mosdepth`` rules according to ``snakemake`` etiquette #636 * Order of columns in QC and coverage report issue #601 * ``delly`` not showing in workflow at runtime #644 @@ -473,7 +474,7 @@ Fixed: ^^^^^^ * umi_workflow config json is set as true for panel and wgs as false. -* Rename umiconsensus bam file headers from {samplenames} to TUMOR/NORMAL. +* Rename umiconsensus bam file headers from {samplenames} to TUMOR/NORMAL. * Documentation autobuild on RTFD @@ -497,7 +498,7 @@ Removed Fixed ^^^^^ -* Fixed issue 577 with missing ``tumor.merged.bam`` and ``normal.merged.bam`` +* Fixed issue 577 with missing ``tumor.merged.bam`` and ``normal.merged.bam`` * Issue 448 with lingering tmp_dir. It is not deleted after analysis is properly finished. Changed @@ -557,7 +558,7 @@ Changed * Update FastQC to 0.11.9 PR #532 * Update BCFTools to 1.11 PR #537 * Update Samtools to 1.11 PR #537 -* Increase resources and runtime for various workflows in PRs #482 +* Increase resources and runtime for various workflows in PRs #482 * Python package dependenicies versions fixed in PR #480 * QoL changes to workflow in series of PR #471 * Series of documentation updates in PRs #489 #553 diff --git a/tests/conftest.py b/tests/conftest.py index bd5bd2b9d..3a6ac097f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -12,7 +12,6 @@ from .helpers import ConfigHelper from BALSAMIC.commands.base import cli from BALSAMIC import __version__ as balsamic_version -from BALSAMIC.utils.models import BalsamicConfigModel MOCKED_OS_ENVIRON = "os.environ"