docs: update balsamic method version in bumpversion #930
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ashwini06
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hassanfa,
khurrammaqbool and
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ashwini06
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## master #930 +/- ##
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Coverage 99.25% 99.25%
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Files 29 29
Lines 1749 1749
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rannick
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May 23, 2022
* edit version in balsamic methods * update bumpeversion list for version changes * change log update
rannick
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Jun 7, 2022
* add option for analysis workflow to config case * add analysis workflow to constants * add analysis workflows to models * add conditions to balsamic workflow * modify multiqc condition for umi * modify condition for umi files * add default analysis workflow to qc_config * modify test models * add analysis workflow for pon to work fine * change balsamic_umi to balsamic-umi * black format pon config file * update Changelog * add balsamic-qc as analysis_workflow option, remove qc config * add analysis workflow cli option to deliver * formatting and adding analysis workflow as argument for get_snakefile * adapt test configs * adapt qc tests * add analysis_workflow in deliver.py * add analysis_workflow in status.py * modify test get snakefile * remove cli option analysis_type of deliver * change run analysis to infer the snakefile workflow from the config file * change the check for reference_genome as the error message was always triggered without consequences * remove analysis-type in invoke.cli * GENOME_VERSION needs to be set up for rules, so set to the different genome version instead of always hg19 * update changelog * feat: add qc only workflow (#847) * 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> * docs: add annotation resources (#916) * 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 * feat: update delly (#920) * update delly to 0.9.1 * update changelog * update changelog * fix Dockerfile * fix Dockerfile * remove OMP * add OMP * remove OMP * add OMP * fix: Change of gnomad pop freq value for UMI workflow (#919) * 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 * feat: add Delly CNV for tumor only workflow (#923) * update changelog * add tumor only cnv analysis and fix messeges in rules * fix messege text * update BALSAMIC documentation * feat: add delly CNV read-depth profile (#924) * update changelog * update changelog * add copy-number profile to delly tumor only * add copy-number profile to delly tumor only * refactor: Remove gatk haplotypcaller (#922) * 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 * refactor: balsamic containers (#921) * 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 * refactor: Update the list of files to be stored and delivered (#915) * feat: bcftools counts QC validation (#925) * Bump version: 8.2.10 → 9.0.0 * docs: balsamic fix styling (#926) * fix balsamic docs styling * fix identattion * remove Admonitions * fix typo * fix: align qc container (#928) * revert csvkit to align_qc container * update changelog * add PR no. to changelog * Bump version: 9.0.0 → 9.0.1 * add option for analysis workflow to config case * add analysis workflow to constants * add analysis workflows to models * add conditions to balsamic workflow * modify multiqc condition for umi * modify condition for umi files * add default analysis workflow to qc_config * modify test models * add analysis workflow for pon to work fine * docs: update balsamic method version in bumpversion (#930) * edit version in balsamic methods * update bumpeversion list for version changes * change log update * change balsamic_umi to balsamic-umi * black format pon config file * Update CHANGELOG.rst (#931) * update Changelog * add balsamic-qc as analysis_workflow option, remove qc config * add analysis workflow cli option to deliver * formatting and adding analysis workflow as argument for get_snakefile * adapt test configs * adapt qc tests * add analysis_workflow in deliver.py * add analysis_workflow in status.py * modify test get snakefile * remove cli option analysis_type of deliver * change run analysis to infer the snakefile workflow from the config file * change the check for reference_genome as the error message was always triggered without consequences * remove analysis-type in invoke.cli * GENOME_VERSION needs to be set up for rules, so set to the different genome version instead of always hg19 * formatting * formatting * update CHANGELOG * update CHANGELOG * black formatting * change GENOME_VERSION to config[reference][genome_version] * add link to PR in CHANGELOG * add quality metrics in QC workflow * add error when canfam3 is used with BALSAMIC main workflow * update input stats files for collect_custom_qc_metrics rule * update changelog Co-authored-by: ashwini06 <ashwini.jeggari@scilifelab.se> Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> Co-authored-by: Khurram Maqbool <khurram.maqbool@outlook.com> Co-authored-by: ivadym <vadym.ivanchuk@scilifelab.se>
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