feat: release 9.0.0 #902
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feat: release 9.0.0 #902
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refactor: umi intervalbed
Conflicts: CHANGELOG.rst
* feat: add canfam3 reference files * feat: add canfam3 reference files, fix test * feat: add canfam3 reference files, fix test * modify CHANGELOG.rst with updates * snakefile is assigned in initialize * Snakefile is not defined in as a -s cli option but as following the call of init and --genome-version * black linting * Update BALSAMIC/constants/reference.py Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * Update BALSAMIC/constants/reference.py Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * Update BALSAMIC/utils/cli.py Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * Update BALSAMIC/workflows/reference-canfam3.smk Co-authored-by: Hassan Foroughi <hassanfa@users.noreply.github.com> * implemented comments * implemented comments, linted * functions get_md5 and create_md5 in utils/cli.py and tests for cosmic key provided for non canfam3 genome-version * linting * add tests for get_md5 and create_md5 * change md5 to sha512 and cosmic key log error * modify md5 return to sha512 * linting * slight change in formatting * sha512 to crc32/md5 * Update BALSAMIC/workflows/reference-canfam3.smk Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * Update BALSAMIC/workflows/reference-canfam3.smk Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * hash->hashed and remove sequencing_type as input for get_snakefile * remove unused sequencing_type Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> Co-authored-by: Hassan Foroughi <hassanfa@users.noreply.github.com>
feat: report umi duplication rate
* version independent panel bed names * default conditions for panel qc validation
Codecov Report
@@ Coverage Diff @@
## master #902 +/- ##
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- Coverage 99.61% 99.25% -0.36%
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Files 29 29
Lines 1816 1749 -67
==========================================
- Hits 1809 1736 -73
- Misses 7 13 +6
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* remove MSK_impact files from config * remove strelka and pindel from config analysis * remove strelka and pindel from balsamic env variables * remove strelka,mutect and baserecalibator from cluster json * remove strelka and pindel from constants * update changelog
* update changelog * update changelog * remove bcftools_stats * add bcftools_stats * update changelog * add bcftools +counts to end point VCFs * update black linter * remove bcftools counts for VCFs not to be uploaded to scout * remove bcftools counts for VCFs not to be uploaded to scout * update changelog
* add balsamic method description * add svdb to softwares * update changelog * adding more text * add wgs sentieon descr * add sentieon filter text * add spell and grammer checks * update changelog * spell and grammer checks for balsamic filters * small text replacemnets * add svdb citation * fix review comments-1 * fix review comments-2 * fix review comments-3 * edit methods text * few more text edits
* update changelog * add ascatngs copynumber file * add ascat to copynumber output * fix fpdf2 to version 2.4.6
* feat: add qc only workflow * conftest qc config * formatting * fixing code smells and attemps to reduce duplication * formatting * remove qc_config container version * formatting * fix qc test * fix qc test * test fixing * test fixing * formatting * draft pytest qc * feat: add qc only workflow * conftest qc config * formatting * fixing code smells and attemps to reduce duplication * formatting * remove qc_config container version * formatting * fix qc test * fix qc test * test fixing * test fixing * formatting * draft pytest qc * black linting + removing test_config_qc_graph_value_error * add container version in qc * add tests for QC graph generation and ValueError * black * upgrade black because of click update and remove unused config_dick in conftest * update black in github action * remove benchmark plot for qc * address duplication * changelog and conftest update * Apply suggestions from code review Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * balck upgrade in changelog * remove variable germline_call_samples as only qc * Update BALSAMIC/workflows/QC.smk Remove chromlist Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * Revert "changelog and conftest update" This reverts commit fabddaf. * remove umiworkflow and vcf from qc * remove bedchrom from qc workflow * update to CHANGELOG from black version * add canfam3 to workflow qc test * remove unused import * remove wgs from qc workflow and modify command to qc_panel * add qc_panel to click * adapt conftest to qc_panel * adapt to qc_panel * use qc_panel also in get_snakemake instead of only qc and models.py comments * modidy test_utils to qc_panel * qc metrics * keep chr in refGene as ref fasta uses chr * add more memory to picard for canfam3 because dogs have 38 chromosomes * no analysis_specific_results in QC.sml * stop removing chr with canfam3 references Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com>
* add ascat to copynumber file * update changelog * add balsamic annotation resources to docs * update changelog * fix review suggestion * modify description for CLNACC * modify description for COSMIC_CNT * modify description for COSMIC_CNT
* update delly to 0.9.1 * update changelog * update changelog * fix Dockerfile * fix Dockerfile * remove OMP * add OMP * remove OMP * add OMP
* add new gnomad pop freq for umi workflow * edit balsamic filters docs * update changelog * fix ident * fix typo * add pop_freq_umi to model attributes * fix indentation * add review suggestions * add PR number to changelog
* update changelog * add tumor only cnv analysis and fix messeges in rules * fix messege text * update BALSAMIC documentation
* update changelog * update changelog * add copy-number profile to delly tumor only * add copy-number profile to delly tumor only
* remove gatk haplotypecallers * remove haplotypecaller and tnsnv from cluster json * remove haplotypecaller from models * remove haplotypecaller from workflow params * remove haplotypcaller and tnsnv from analysis json * remove unused callers from tests * update changelog
* update align_qc base image * update align_qc tool versions * add tabix version * remove csvkit from align_qc * remove csvkit frm bioinfo_tool env * update align _qc container tool versions in readthedocs * add samtools versions to tests * update changelog * update base image in coverage_qc container * update tool versions in cover_qc container * update tool versions in bioinfo softwares docs * update changelog * update base image in container varcall_cnvkit * update cnvkit version * update purecn version and lock bcftools and tabix versions * update docs and changelog * update base image in varcall_py36 container * update tools in varcall_py36 * update samtools version in docs * update changelog * update base image of annotate container * update ensembl vep in annotate container * update readthedocs for vep version * update changelog * fix typo in varcall_py27
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Kudos, SonarCloud Quality Gate passed!
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ivadym
approved these changes
May 2, 2022
khurrammaqbool
approved these changes
May 2, 2022
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This PR:
Creates a new release of v9.0.0
Added:
^^^^^^
.cghfiles fromCNVkitoutputs vcf2cytosure #858<case>_metrics_deliverables.yamlfeat: extract additional WGS metrics #907NUMBER_OF_SITES(bcftoolscounts) feat: bcftools counts QC validation #925Changed:
^^^^^^^^
gnomad_pop_freqvalue is changed from0.005to0.02fix: Change of gnomad pop freq value for UMI workflow #919collect_custom_qc_metricsrule frommultiqc.rulefeat: bcftools counts QC validation #925Fixed:
^^^^^^
collect_qc_metrics.pyfailing for WGS cases with emptycapture_kitargument fix: capture kit empty argument for WGS runs #850fpdf2to2.4.6Delete the report generation workflow in BALSAMIC #878Removed
^^^^^^^
--qc-metrics/--no-qc-metricsflag from thebalsamic report delivercommand refactor: merge QC metric extraction workflows #833MSK_impactandMSK_impact_noStrelkajson files from configstrelka,pindel,mutect2variables from BALSAMIC<case>_qc_report.htmlfile) Delete the report generation workflow in BALSAMIC #878--sample-id-mapand--case-id-mapflags from thebalsamic report delivercommand Delete the report generation workflow in BALSAMIC #878gatk_haplotypecallerfor reporting panel germline variants Refactor: Remove second germlinecaller haplotypecaller #918To Do on CG
^^^^^^^^^^
.cghfile to Scout. Related to Support .cgh file uploads to Scout for BALSAMIC analysis cg#1437Review and tests: