Release/8 0 0 #674
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Release/8 0 0 #674
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* add new option umi_post_process * CHANGELOG.rst
#635) * all vars in filtered and not just PASS * changelog
* refactor align rules * fix bwa_mem indent * update changelog * fix picard markdups rulename * fix changelog message * changelog edits
* add samtools to qc * changelog * threads * sm etiquette * review comments * params sample * move samtools stats back to align rules * change stats to picard_stats
* refactor rules and standard triple quote shell * refactor according to comments * changelog * changelog * multiline
* changelog * params
* manta sv filters * changelog * add filtered manta to output * correct input tag in shell * deliver svs * changelog
* manta sv filters * changelog * add filtered manta to output * correct input tag in shell * deliver svs * changelog * reformat
* add vcf2cytosure as pip dependency * ignore pip installs in conda env * changelog
* cleanup old files * restore balsamic.yaml * changelog
* changelog * update actions * changelog * path-->paths * changelog * fix typo in github actions
* add git to Dockerfile to be able to install from git * changelog * added egg to pip
* add purecn dependencies * update changelog * add optparse to dependencies
* fixed order of id and type * changelog * trailing space
* update changelog * fix shell comments * remove cnvkit calling for wgs runs * update changelog * add option threads
* Update GNOMAD URL * Update changelog
* Add Delly https://github.com/dellytools/delly [issue 644 ] * Update changelog * remove centel temporarily * remove dummy container * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly exclusion regions * Add delly container * Add delly container * Add delly container * Add delly container * Add delly container * Feat/add Delly container (#648) * Add delly container * Add delly container * Add delly container * Add delly container * Add delly container * Add delly container * Add delly container * empty space * Add delly container Co-authored-by: hassanfa <hassan.foroughi@gmail.com> * Add bcf to vcf.gz command for delly * Add bcf to vcf command * Add bcftools to delly container * Add filter command to delly * Update BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule Co-authored-by: Hassan Foroughi <hassanfa@users.noreply.github.com> * Fix renamed file to delly_exclusion.tsv * Fix removed contents of file delly_exclusion.tsv * Add tabix to delly container * Fix refactor delly and manta rules * Fix rename dly_excl to delly_exclusion * Update changelog * Update BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule * Update BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule * Update CHANGELOG.rst * Fix delly output file * Fix genome_version "hg38" for delly_exclusion * Update changelog * Add prepare_delly_exclusion rule * Update changelog * Update CHANGELOG.rst * Add delly_exclusion_converted.tsv file * Add delly to docs Co-authored-by: hassanfa <hassan.foroughi@gmail.com> Co-authored-by: Hassan Foroughi <hassanfa@users.noreply.github.com>
* Fix delly run * changelog * Fix delly * fix delly models and vep
* add info sentieon export to doc * update changelog * fix case converter to word Balsamic
* fix sampleids * changelog
* fixed links for ascatngs documentation * Fix ascat links
* Add ascat tumor normal rule * disable conda for ascat * changelog * remove ascat from conda container list * added init file for ascat dummy container Co-authored-by: Khurram Maqbool <khurram.maqbool@hasta.scilifelab.se>
* fix space in reference json * add changelog
… container build (#706) * changelog * Fix py36 containder * Fix typo * parse conda package name for channel::package format * changelog * Fix typo * changelog * changelog * changelog * changelog * fix package channels * fix package version conflicts * Fix package versions to resolve conflicts * Fix newline error at end of file * Fix package channels and cleanup * update container python version * remove python * Fix bcftools version * Fix bcftools version * Fix bcftools version * Fix bcftools and tabix version * Fix tabix version * Add python 3.6 to delly container * Add pip * Cleanup delly container * Add package channel * Fix package channels * Fix package channels * Fix channels for align_qc container * Fix channels for varcall_cnvkit container * Fix channels for annotate container * Fix all channels for annotate container * Remove channel check. All packages must have channel * Add dummy channel for ascat * Add channel to python package * always run testing container Co-authored-by: hassanfa <hassan.foroughi@gmail.com>
* changelog * add convert inversions and bgzip vcf file to manta rules * add convert inversions and bgzip vcf file to manta tumor only rule * bgzip converted manta vcf files
* refactor umi snakemakerules * refactor variant calling rules-batch1 * fix changelog * fix errors caused pytest failures * export sentieon-lic * uncomment lines * fix message descriptions * expand ml in message * fix review comments * fix sentieon positional args * fix pytests invalid escape sequence warnings * refactor few more variantcalling rules * refactor somatic sv rules * add sentieon temp directories to umi rules
* refactor annotation rules according snakemake git etiquette * update changelog * fix full abbreviations * replace message text with case name * refactored names in default_rules_to_deliver * add issues links to changelog * fix changelog * change tumoronly to tumor_only
* refactor rule for cnvkit paired analysis * fix changelog * add sampleid to params * add changelog * fix commented lines
* update snakemake to v6.5.3 * changelog
* convert SV to CNV in ascat rule * add sequencing type to variant callers * add sequencing type to models * add seq type condition * generalize all SV results * update tests to match new changes * Run container test workflow always * always run testing container * ngs filter for CNVkit * change panel to targeted * constant instead of duplicated list * use analysis_type from config * proper negative test :-p * move common sections together * added missing wgs sv tumor only file * add missing sv wgs tumor normla filter rule * changelog * tumor-only ngs filter manta and delly * fix minor bug * docstring review comment * enable delly for ngs filters * review comments
* refactor quality control rules according to snakemake etiquette * update changelog * refactor dragen rule * add message to variantcalling splitbed rule * finalcheck- fix spaces for multiple rules
* new location for submodules * split conda and non-conda parsing * formatting * remove redundancy, and one single bioinfo dict * changelog * code smell and some tsts * redundant lines removed * a bit more verbose * remove allelecount * Update CHANGELOG.rst 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/utils/cli.py Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com> * address code smell * redundant continue Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com>
* add citation.cff * codeowner * changelog * format yml files * update list
* change constants as params across snakemake rules * add more params as constants from balsamic workflow * use single workflow params models * remove extra params in vep to constants * refactor and add new tests to models * move param pcr_indel to constants * update changelog * cleanup and fix pytest error * fix code smells with new class names * cleanup and fix docstring * fix indentation in model classes
* blacklinter * format with black * add black to dev list * black * more formatting * python version to 3.7.9 * fix python version * remove python matrix * remove container workflows temporarily * remove fixed version for pip * changelog * fix black version * lock black linter version in action * black lint it * install dev requirments after installing balsamic * pytest dev install as its own step * unique name for pytest step * bring back container workflows * review comments * update docs
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This PR:
[8.0.0]
Added:
samtoolsflagstats and stats to workflow and MultiQCdelly v0.8.7somatic SV caller Add Delly #644dellycontainter Add Delly #644bcftools v1.12todellycontainer Add Delly #644tabix v0.2.6todellycontainer Add Delly #644vcf2cytosureto annotate containergitto the container definitionPureCNrpackage incnvkitcontainerPureCNforcnvkitcallascatngsas a submodule Add ascat reference files to cancer/references, container and tumor-normal rule #672ascatngscontainerdocs/FAQ.rstascatngsdownload references from reference_file repository Add ascat reference files to cancer/references, container and tumor-normal rule #672dellytumor only rule Add Delly #644ascatngsdownload container Add ascat reference files to cancer/references, container and tumor-normal rule #672bashrcascatngstumor normal rule for wgs cases Add ascat reference files to cancer/references, container and tumor-normal rule #672mantaconvert inversion Manta convert inversions #709CITATION.cffto cite BALSAMICChanged:
MarkDuplicatestopicard_markduplicatesinbwa_memrule andcluster.jsonGATK_contesttogatk_contestdocs/**andCHANGELOG.rstchangessnakemaketov6.5.3Upgrade snakemake to 6.5.3 #501GNOMADURLcnvkit batchinto individual commandscnvkit batchinto individual commandsBlackfrom YAPF #619Fixed:
annotaterules according to snakemake etiquette Refactor rules according BALSAMIC's Snakemake etiquette #636alignrules according to snakemake etiquette Refactor rules according BALSAMIC's Snakemake etiquette #636fastqcvepcontest andmosdepthrules according tosnakemakeetiquette Refactor rules according BALSAMIC's Snakemake etiquette #636dellynot showing in workflow at runtime Add Delly #644ascatngsdocumentation links inFAQsAdd ascat reference files to cancer/references, container and tumor-normal rule #672varcall_py36container build and push Failed run for Docker image build push varcall_py36 #703quality controlrules according to snakemake etiquette Refactor rules according BALSAMIC's Snakemake etiquette #636Removed:
To Do:
cnvkit.pairedrule. Split batch to individual commandsBlackfrom YAPF #619Review and tests: