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Add vcf2cytosure as dependency #650

Merged
merged 3 commits into from
Jun 14, 2021
Merged

Add vcf2cytosure as dependency #650

merged 3 commits into from
Jun 14, 2021

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hassanfa
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@hassanfa hassanfa commented Jun 14, 2021 •
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This PR:

Added:

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@hassanfa hassanfa marked this pull request as ready for review June 14, 2021 10:55
@hassanfa hassanfa requested a review from ashwini06 as a code owner June 14, 2021 10:55
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Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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codecov bot commented Jun 14, 2021 •
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Codecov Report

Merging #650 (d32a04f) into develop (daaccf2) will increase coverage by 0.00%.
The diff coverage is 100.00%.

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@@           Coverage Diff            @@
##           develop     #650   +/-   ##
========================================
  Coverage    98.93%   98.94%           
========================================
  Files           26       26           
  Lines         1697     1699    +2     
========================================
+ Hits          1679     1681    +2     
  Misses          18       18
Flag Coverage Δ
unittests 98.94% <100.00%> (+<0.01%) ⬆️

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Impacted Files Coverage Δ
BALSAMIC/utils/cli.py 99.36% <100.00%> (+<0.01%) ⬆️

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ashwini06
ashwini06 reviewed Jun 14, 2021
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👍 May I know where in the rules, vcf2cytosure command is utilized?

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hassanfa commented Jun 14, 2021 •
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👍 May I know where in the rules, vcf2cytosure command is utilized?

That's the other PR I have not opened yet. I needed a prebuilt container first.

@hassanfa hassanfa merged commit c76a3dd into develop Jun 14, 2021
@hassanfa hassanfa deleted the feat/add_vcf2cytosure branch June 14, 2021 12:40
hassanfa added a commit that referenced this pull request Aug 26, 2021
@hassanfa @ashwini06
@khurrammaqbool @ivadym
Release/8 0 0 (#674)
05646bc 
* Fix/umi post process (#633)

* add new option umi_post_process

* CHANGELOG.rst

* Include all filtered variants in vcf-filtered-clinical not just PASSed (#635)

* all vars in filtered and not just PASS

* changelog

* refactor align rules (#638)

* refactor align rules

* fix bwa_mem indent

* update changelog

* fix picard markdups rulename

* fix changelog message

* changelog edits

* Add samtools stats to QC steps (#639)

* 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 vep, fastqc, mosdepth, and contest rules (#637)

* refactor rules and standard triple quote shell

* refactor according to comments

* changelog

* changelog

* multiline

* Additional filter for tumor-normal calls in VarDict (#643)

* changelog

* params

* Feat/deliver sv (#634)

* manta sv filters

* changelog

* add filtered manta to output

* correct input tag in shell

* deliver svs

* changelog

* Revert "Feat/deliver sv (#634)" (#646)

This reverts commit b2c83e2.

* Second try: Feat/deliver sv (#647)

* manta sv filters

* changelog

* add filtered manta to output

* correct input tag in shell

* deliver svs

* changelog

* reformat

* Add vcf2cytosure as dependency (#650)

* add vcf2cytosure as pip dependency

* ignore pip installs in conda env

* changelog

* cleanup unused container conda (#649)

* cleanup old files

* restore balsamic.yaml

* changelog

* Avoid running pytest when changelog or docs are updated (#651)

* changelog

* update actions

* changelog

* path-->paths

* changelog

* fix typo in github actions

* add git to containers (#652)

* add git to Dockerfile to be able to install from git

* changelog

* added egg to pip

* add purecn dependencies (#657)

* add purecn dependencies

* update changelog

* add optparse to dependencies

* Fix/issue 601 (#659)

* fixed order of id and type

* changelog

* trailing space

* add purecn in configs

* refactor cnvkit single rule

* cnvkit refactor changelog (#663)

* update changelog

* fix shell comments

* remove cnvkit calling for wgs runs

* update changelog

* add option threads

* Update GNOMAD URL [Issue 664] (#665)

* Update GNOMAD URL

* Update changelog

* Add Delly somatic SV caller [issue 644 ] (#645)

* 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>

* Update CODEOWNERS (#667)

* Update docs to add reference section in FAQ

* Update changelog

* changelog

* chanloge

* Update FAQs.rst

* Update FAQs.rst code blocks

* Update FAQs.rst

* Update FAQs highlights

* Update FAQs highlights

* add ascatngs as submodule and fixing tests (#668)

* add ascatngs as submodule

* remove wrong module file

* added github actions and container

* recursive submodule

* ascat docker on push or pr

* fix chanloge format

* with clause

* update build only for push

* fix typoe in ascat name

* add context to workflow instead of path

* add docker action on release, develop, master, push, and pr for modules

* change keyword

* change keyword from pullrequets to pullrequest

* fix lots of tests for delly and cnvkit

* review comments

* Removed the install.sh script [issue #655] (#676)

* Removed the install.sh script

* Update CHANGELOG

* Optimize TMB calculation (#677)

* calculate tmb

* changelog

* Feat/delly tumor only rule (#681)

* Add delly tumor only rule: clean delly tumor normal rule: refactor manta tumor only rule

* changelog

* Add ascat reference download (#682)

* Add ascat reference download

* changelog

* Fix case and links

* Fix/ascat reference 20210720 (#691)

* fix ascat download link

* changelog

* Feat/ascat download container (#689)

* Add ascat container

* changelog

* remove ascat

* Add ascatngs as submodule

* Add ascatngs

* Fix/delly run (#698)

* Fix delly run

* changelog

* Fix delly

* fix delly models and vep

* Doc/update sentieon info (#697)

* add info sentieon export to doc

* update changelog

* fix case converter to word Balsamic

* Refactor/cnvkit single (#700)

* fix sampleids

* changelog

* fixed links for ascatngs documentation (#702)

* fixed links for ascatngs documentation

* Fix ascat links

* Add ascat tumor normal rule (#699)

* 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 (#705)

* fix space in reference json

* add changelog

* Fix/All containers´ performance improvements and fix for varcall_py36 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>

* Feat/manta convert inversions (#710)

* 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 variantcalling snakemake rules (#701)

* 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 (#696)

* 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 cnvkit paired (#693)

* refactor rule for cnvkit paired analysis

* fix changelog

* add sampleid to params

* add changelog

* fix commented lines

* update snakemake to v6.5.3 (#678)

* update snakemake to v6.5.3

* changelog

* Feat: generalize ascat, delly, and manta  (#708)

* 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 (#712)

* 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

* Refactor bioinfo tools version parsing (#713)

* 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>

* Feat: codeowner (#715)

* add citation.cff

* codeowner

* changelog

* format yml files

* update list

* Refactor/params to constants (#714)

* 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

* Feat/use black lint (#716)

* 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

Co-authored-by: ashwini06 <ashwini06@users.noreply.github.com>
Co-authored-by: ashwini06 <ashwini.jeggari@scilifelab.se>
Co-authored-by: Khurram Maqbool <kmgeneticist@gmail.com>
Co-authored-by: Vadym Ivanchuk <vadym.ivanchuk@gmail.com>
Co-authored-by: Khurram Maqbool <khurram.maqbool@hasta.scilifelab.se>
@ashwini06 ashwini06 mentioned this pull request Mar 1, 2022
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@hassanfa @ashwini06