CHANGELOG.rst

[X.X.X]

Added:

• Fastq concatenation #1069
• CADD SNV references #1126
• CADD SNV annotation #1150
• Samtools stats, flagstat, idxstat to WGS workflow #1176
• Functionality for dynamically assigning fastq-info to sample dict in config from input fastq-dir #1176
• Annotate SNVs with cancer germline SNV observations from loqusDB #1178
• Annotate SNVs with somatic SNV observations from loqusDB #1187
• Tests for Annotation with Cancer germline, somatic and clinical observations, and swegen frequencies https://github/Clinical-Genomics/BALSAMIC/pull/1190
• Annotate SVs with somatic SV observations from loqusDB #1194
• Support singularity bind paths with different destination directories https://github/Clinical-Genomics/BALSAMIC/pull/1211
• Added --rerun-trigger mtime option to Snakemake command #1217
• CADD container #1222
• Container ettiquette to ReadtheDocs #1132
• htslib (samtools, bcftools tabix) container #1234
• Release version support for cache generation #1231
• CADD scores for INDELs #1238
• CADD reference to tests https://githuc.com/Clinical-Genomics/BALSAMIC/pull/1241
• Add cache version option to config case #1244
• cnvkit container #1252
• PureCN container #1255
• Resolved FASTQ paths to sample dictionary (balsamic logging) #1275

Changed:

• Changed CN header field in cnvpytor in cnvpytor_tumor_only to be Float instead of Integer #1182
• Changed samples in case_config.json from being a dict to a list of dicts #1176
• Updated snakemake version to 7.25.0 #1099
• Updated cryptography version to 41.0.1 #1173
• Refactor bam and fastq inputs in snakemake to call pydantic model functions #1176
• Standardised alignment workflows to WGS-workflow #1176
• Implemented parallel trimming and alignment in all workflows per lane #1176
• All bam-QC tools take the final dedup.realign bamfile as input #1176
• Validation of pydantic models done both during config and run #1176
• Refactored fastp rules, and changed order of UMI-trimming and quality trimming #1176
• Fix pydantic version (<2.0) #1191
• Refactor constants #1174
• Move models to their own folder #1176
• Balsamic init workflow refactoring #1188
• Updated cryptography version to 41.0.2 #1205
• Refactor snakemake executable command generation https://github/Clinical-Genomics/BALSAMIC/pull/1211
• Updated Python version to 3.11 and its dependencies #1216
• Tools versions in doc https:/github.com/Clinical-Genomics/BALSAMIC/pull/1239
• Reuse common Balsamic CLI options #1242
• Update reference.json file to use relative paths #1251
• Update pydantic to v2 while maintaining support for v1 models #1253
• PCT_PF_READS_IMPROPER_PAIRS QC threshold lowered to 5% #1265
• Migrate cache models to pydantic v2 #1277

Fixed:

• vcf2cytosure container #1159
• Link external fastqs to case folder & create case directory #1195
• vcf2cytosure container missing constants #1198
• Bash commands in vep_somatic_clinical_snv #1200
• Fix SVDB annotation intermediate rule #1218
• Broken documentation links #1226
• Updated contributors in main README #1237
• CNVpytor container #1246
• Restored balsamic container in UMI concatenation rule #1261
• CNVpytor container, fixing numpy version #1273

Removed:

• Config folder #1175
• Quality trimming of fastqs for UMI workflow #1176
• Balsamic container #1230
• Plugin CLI #1245
• Realignment step for TGA workflow #1272

[12.0.2]

Fixed:

• Missing Number in VCF header for SVs #1203

Changed:

• Fix cyvcf2 to version 0.30.22 #1206
• Fix pydantic version (<2.0) #1206
• Update varcall-cnvkit container versions #1207

[12.0.1]

Added:

• WGS QC criteria for PCT_PF_READS_IMPROPER_PAIRS (condition: <= 0.1) #1164

Fixed:

• Logged version of Delly (changing it to v1.0.3) #1170

[12.0.0]

Added:

• PIP specific missing tools to config #1096
• Filtering script to remove normal variants from TIDDIT #1120
• Store TMB files in HK #1144

Changed:

• Fixed all conda container dependencies #1096
• Changed --max_sv_size in VEP params to the size of chr1 for hg19 #1124
• Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours #1143
• Update cosmicdb to v97 #1147
• Updated read the docs with the changes relevant to mention #1153

Fixed:

• Update cryptography version (39.0.1) due to security alert #1087
• Bump cryptography to v40.0.2 and gsutil to v5.23 #1154
• Pytest file saved in balsamic directory #1093
• Fix varcall_py3 container bcftools dependency error #1097
• AscatNgs container #1155

[11.2.0]

Fixed:

• Number of variants are increased with triallelic_site #1089

[11.1.0]

Added:

• Added somalier integration and relatedness check: #1017
• Cluster resources for CNVPytor tumor only #1083

Changed:

• Parallelize download of reference files #1065
• Parallelize download of container images #1068

Fixed:

• triallelic_site in quality filter for SNV #1052
• Compression of SNV, research and clinical, VCF files #1060
• test_write_json failing locally #1063
• Container build and push via github actions by setting buildx provenance flag to false #1071
• Added buildx to the submodule workflow #1072
• Change user in somalier container to defaultuser #1080
• Reference files for hg38 #1081

[11.0.2]

Changed:

• Code owners #1050

Fixed:

• MaxDepth in quality filter for SV #1051

[11.0.1]

Fixed:

• Incorrect raw TNscope VCF delivered #1042

[11.0.0]

Added:

• Use of PON reference, if exists for CNVkit tumor-normal analysis #982
• Added PON version to CLI and config.json #983
• cnvpytor to varcallpy3 container #991
• cnvpytor for tumor only workflow #994
• R packages to cnvkit container #996
• Missing R packages to cnvkit container #997
• add rlang to cnvkit container #998
• AnnotSV and bedtools to annotate container #1005
• cosmicdb to TNscope for tumor only and tumor normal workflows #1006
• loqusDB dump files to the config through the balsamic config case CLI #992
• Pre-annotation quality filters for SNVs annd added research to output files #1007
• Annotation of snv_clinical_observations for somatic snv #1012
• Annotation of sv_clinical_observations for somatic sv and SV CNV filter rules #1013
• Swegen SNV and SV frequency database for WGS #1014
• triallelic_sites and variants with MaxDepth to the VCFs #1021
• Clinical VCF for TGA workflow #1024
• CNVpytor plots into the CNV PDF report #1023
• Research and clinical housekeeper tags #1023
• Cluster configuration for rules #1028
• Variant filteration using loqusDB and Swegen annotations #1029
• Annotation resources to readsthedocs #1031
• Delly CNV rules for TGA workflow #103
• cnvpytor container and removed cnvpytor from varcallpy3 #1037

Changed:

• Added version number to the PON reference filename (.cnn) #982
• Update TIDDIT to v3.3.0, SVDB to v2.6.4, delly to v1.1.3, vcf2cytosure to v0.8 #987
• toml config file for vcfanno #1012
• Split vep_germline rule into tumor and normal #1018
• Extract number of variants from clinical files #1022

Fixed:

• Reverted pandas version (from 1.3.5 to 1.1.5) #1018
• Mate in realigned bam file #1019
• samtools command in merge bam and names in toml for vcfanno #1020
• If statement in vep_somatic_clinical_snv rule #1022
• Invalid flag second of pair validation error #1025
• Invalid flag second of pair validation error using picardtools #1027
• Samtools command for mergetype tumor #1030
• varcall_py3 container building #1036
• Picard and fastp commands params and cluster config for umi workflow #1032
• Set channels in varcall_py3 container #1035
• Delly command for tumor-normal analysis #1039
• tabix command in bcftools_quality_filter_TNscope_umi_tumor_only rule #1040

Removed:

• case ID from the PON .cnn output file #983
• TNhaplotyper for paired WGS analysis #988
• TNhaplotyper for tumor only WGS analysis #1006
• TNhaplotyper for TGS #1022

[10.0.5]

Changed:

• Update vcf2cytosure version to v0.8 #1010
• Update GitHub action images to ubuntu-20.04 #1010
• Update GitHub actions to their latest versions #1010

[10.0.4]

Fixed:

• Increase sambamba_exon_depth rule run time #1001

[10.0.3]

Fixed:

• Input VCF files for cnvkit rules, cnvkit command and container #995

[10.0.2]

Fixed:

• TIDDIT delivery rule names (undo rule name changes made in Balsamic 10.0.1) #977
• BALSAMIC readthedocs CLI documentation generation #965

[10.0.1]

Fixed:

• Command and condition for TIDDIT and fixed ReadtheDocs #973
• ReadtheDocs and updated the header #973

Changed:

• Time allocation in cluster configuration for SV rules #973

[10.0.0]

Added:

• New option analysis-workflow to balsamic config case CLI #932
• New python script to edit INFO tags in vardict and tnscope_umi VCF files #948
• Added cyvcf2 and click tools to the varcallpy3 container #948
• Delly TIDDIT and vcf2cytosure for WGS #947
• Delly TIDDIT vcf2cytosure and method to process SVs and CNVs for WGS #947
• SV and CNV analysis and TIDDIT to balsamic ReadtheDocs #951
• Gender to config.json #955
• Provided gender as input for vcf2cyosure #955
• SV CNV doc to balsamic READTHEDOCS #960
• Germline normal SNV VCF file header renaming to be compatible with genotype uploads #882
• Add tabix and gzip to vcf2cytosure container #969

Changed:

• UMI-workflow for panel cases to be run only with balsamic-umi flag #896
• Update codecov action version to @v2 #941
• QC-workflow for panel cases to be run only with balsamic-qc #942
• get_snakefile function takes the argument analysis_workflow to trigger the QC workflow when necessary #942
• bcftools_counts input depending on analysis_workflow #942
• UMI output filename TNscope_umi is changed to tnscope_umi #948
• Update delly to v1.0.3 #950
• Update versions of delly in ReadtheDocs #951
• Provided gender as input for ascat and cnvkit #955
• Update QC criteria for panel and wgs analysis according to https://github.com/Clinical-Genomics/project-planning/issues/338#issuecomment-1132643330. #952
• For uploads to scout, increasing the number of variants failing threshold from 10000 to 50000 #952

Fixed:

• GENOME_VERSION set to the different genome_version options and replaced with config["reference"]["genome_version"] #942
• run_validate.sh script #952
• Somatic SV tumor normal rules #959
• Missing genderChr flag for ascat_tumor_normal rule #963
• Command in vcf2cytosure rule and updated ReadtheDocs #966
• Missing name analysis_dir in QC.smk #970
• Remove sample_type wildcard from the vcfheader_rename_germline rule and change genotype file name #971

Removed

• Removed qc_panel config in favor of standard config #942
• Removed cli --analysis_type for balsamic report deliver command and balsamic run analysis #942
• Removed analysis_type: qc_panel and replace the trigger for QC workflow by analysis_workflow: balsamic-qc #942
• Outdated balsamic report files (balsamic_report.html & balsamic_report.md) #952

[9.0.1]

Fixed:

• Revert csvkit tool in align_qc container #928
• Automatic version update for balsamic methods #930

[9.0.0]

Added:

• Snakemake workflow to create canfam3 reference #843
• Call umi variants using TNscope in bed defined regions #821
• UMI duplication metrics to report in multiqc_picard_dups.json #844
• Option to use PON reference in cnv calling for TGA tumor-only cases #851
• QC default validation conditions (for not defined capture kits) #855
• SVdb to the varcall_py36 container #872
• SVdb to WGS workflow #873
• Docker container for vcf2cytosure #869
• Snakemake rule for creating .cgh files from CNVkit outputs #880
• SVdb to TGA workflow #879
• SVdb merge SV and CNV #886
• Readthedocs for BALSAMIC method descriptions #906
• Readthedocs for BALSAMIC variant filters for WGS somatic callers #906
• bcftools counts to varcall filter rules #899
• Additional WGS metrics to be stored in <case>_metrics_deliverables.yaml #907
• ascatNGS copynumber file #914
• ReadtheDocs for BALSAMIC annotation resources #916
• Delly CNV for tumor only workflow #923
• Delly CNV Read-depth profiles for tumor only workflows #924
• New metric to be extracted and validated: NUMBER_OF_SITES (bcftools counts) #925

Changed:

• Merge QC metric extraction workflows #833
• Changed the base-image for balsamic container to 4.10.3-alpine #869
• Updated SVdb to 2.6.0 #901
• Upgrade black to 22.3.0
• For UMI workflow, post filter gnomad_pop_freq value is changed from 0.005 to 0.02 #919
• updated delly to 0.9.1 #920
• container base_image (align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py36) to 4.10.3-alpine #921
• update container (align_qc, annotate, coverage_qc, varcall_cnvkit,varcall_py36) bioinfo tool versions #921
• update tool versions (align_qc, annotate, coverage_qc, varcall_cnvkit) in methods and softwares docs #921
• Updated the list of files to be stored and delivered #915
• Moved collect_custom_qc_metrics rule from multiqc.rule #925

Fixed:

• Automate balsamic version for readthedocs install page #888
• collect_qc_metrics.py failing for WGS cases with empty capture_kit argument #850
• QC metric validation for different panel bed version #855
• Fixed development version of fpdf2 to 2.4.6 #878
• Added missing svdb index file #848

Removed

• --qc-metrics/--no-qc-metrics flag from the balsamic report deliver command #833
• Unused pon option for SNV calling with TNhaplotyper tumor-only #851
• SV and CNV callers from annotation and filtering #889
• vcfanno and COSMIC from SV annotation #891
• Removed MSK_impact and MSK_impact_noStrelka json files from config #903
• Cleanup of strelka, pindel , mutect2 variables from BALSAMIC #903
• bcftools_stats from vep #898
• QC delivery report workflow (generating the <case>_qc_report.html file) #878
• --sample-id-map and --case-id-map flags from the balsamic report deliver command #878
• Removed gatk_haplotypecaller for reporting panel germline variants #918

[8.2.10]

Added:

• libopenblas=0.3.20 dependency to annotate container for fixing bcftools #909

Fixes:

• bcftools version locked at 1.10 #909

Changed:

• base image of balsamic container to 4.10.3-alphine #909
• Replaced annotate container tests with new code #909

Removed:

• Removed failed vcf2cytosure installation from annotate container #909

[8.2.9]

Added:

• Added slurm qos tag express #885
• Included more text about UMI-workflow variant calling settings to the readthedocs #888
• Extend QCModel to include n_base_limit which outputs in config json QC dict

Fixes:

• Automate balsamic version for readthedocs install page #888

Changed:

• Upgrade black to 22.3.0
• fastp default setting of n_base_limit is changed to 50 from 5

[8.2.8]

Added:

• Added the readthedocs page for BALSAMIC variant-calling filters #867
• Project requirements (setup.py) to build the docs #874
• Generate cram from umi-consensus called bam files #865

Changed:

• Updated the bioinfo tools version numbers in BALSAMIC readthedocs #867
• Sphinx version fixed to <0.18 #874
• Sphinx GitHub action triggers only on master branch PRs
• VAF filter for reporting somatic variants (Vardict) is minimised to 0.7% from 1% #876

Fixes:

• cyvcf2 mock import for READTHEDOCS environment #874

[8.2.7]

Fixes:

• Fixes fastqc timeout issues for wgs cases #861
• Fix cluster configuration for vep and vcfanno #857

[8.2.6]

Fixes:

• Set right qos in scheduler command #856

[8.2.5]

• balsamic.sif container installation during cache generation #841

Fixed:

• Execution of create_pdf python script inside the balsamic container #841

[8.2.4]

Added:

• --hgvsg annotation to VEP #830
• ascatNgs PDF delivery (plots & statistics) #828

[8.2.3]

Fixed:

• Add default for gender if purecn captures dual gender values #824

Changed:

• Updated purecn and its dependencies to latest versions

[8.2.2]

Added:

• ascatNGS tumor normal delivery #810

Changed:

• QC metrics delivery tag #820
• Refactor tmb rule that contains redundant line #817

[8.2.1]

Fixed:

• cnvkit gender comparison operator bug #819

[8.2.0]

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
• 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
• Store research VCFs for all filtered and annotated VCF files
• Added .,PASS to all structural variant filter rules to resolve the issues with missing calls in filtered file
• Handling of QC metrics validation errors #783
• Github Action workflow that builds the docs using Sphinx #809
• Zenodo integration to create citable link #813
• Panel BED specific QC conditions #800
• Metric extraction to a YAML file for Vogue #802

Changed:

• refactored main workflow with more readible organization #614
• refactored conda envs within container to be on base and container definition is uncoupled #759
• renamed umi output file names to fix issue with picard HSmetrics #804
• locked requirements for graphviz io 0.16 #811
• QC metric validation is performed across all metrics of each of the samples #800

Removed:

• The option of running umiworkflow independently with balsamic command-line option "-a umi"
• Removed source activate from reference and pon workflows #764

Fixed:

• Pip installation failure inside balsamic container #758
• Fixed issue #768 with missing vep_install command in container
• Fixed issue #765 with correct input bam files for SV rules
• Continuation of CNVkit even if PURECN fails and fix PureCN conda paths #774 #775
• Locked version for cryptography package
• 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 issue #767 for ascatngs hardcoded values
• 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
• 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

[8.1.0]

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
• Added ClinVar as a source to download and to be annotated with VCFAnno #737

Changed:

• Updated docs for git FAQs #731
• Rename panel of normal filename Clinical-Genomics/cgp-cancer-cnvcall#10

Fixed:

• Fixed bug with using varcall_py36 container with VarDict #739
• Fixed a bug with VEP module in MultiQC by excluding #746
• Fixed a bug with bcftools stats results failing in MultiQC #744

[8.0.2]

Fixed:

• Fixed breaking shell command for VEP annotation rules #734

[8.0.1]

Fixed:

• Fixed context for Dockerfile for release content #720

[8.0.0]

Added:

• samtools flagstats and stats to workflow and MultiQC
• delly v0.8.7 somatic SV caller #644
• delly containter #644
• bcftools v1.12 to delly container #644
• tabix v0.2.6 to delly container #644
• Passed SV calls from Manta to clinical delivery
• An extra filter to VarDict tumor-normal to remove variants with STATUS=Germline, all other will still be around
• Added vcf2cytosure to annotate container
• git to the container definition
• prepare_delly_exclusion rule
• Installation of PureCN rpackage in cnvkit container
• Calculate tumor-purity and ploidy using PureCN for cnvkit call
• ascatngs as a submodule #672
• GitHub action to build and test ascatngs container
• Reference section to docs/FAQ.rst
• ascatngs download references from reference_file repository #672
• delly tumor only rule #644
• ascatngs download container #672
• Documentation update on setting sentieon env variables in bashrc
• ascatngs tumor normal rule for wgs cases #672
• 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
• added CITATION.cff to cite BALSAMIC

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
• Avoid running pytest github actions workflow on docs/** and CHANGELOG.rst changes
• Updated snakemake to v6.5.3 #501
• Update GNOMAD URL
• Split Tumor-only cnvkit batch into individual commands
• Improved TMB calculation issue #51
• Generalized ascat, delly, and manta result in workflow. #708
• Generalized workflow to eliminate duplicate entries and code. #708
• Split Tumor-Normal cnvkit batch into individual commands
• Moved params that are used in multiple rules to constants #711
• Changed the way conda and non-conda bioinfo tools version are parsed
• Python code formatter changed from Black to YAPF #619

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 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
• ascatngs documentation links in FAQs #672
• varcall_py36 container build and push #703
• Wrong spacing in reference json issue #704
• Refactor snakemake quality control rules according to snakemake etiquette #636

Removed:

• Cleaned up unused container definitions and conda environment files
• Remove cnvkit calling for WGS cases
• Removed the install.sh script

[7.2.5]

Changed:

• Updated COSMIC path to use version 94

[7.2.5]

Changed:

• Updated path for gnomad and 1000genomes to a working path from Google Storage

[7.2.4]

Changed:

• Updated sentieon util sort in umi to use Sentieon 20201002 version

[7.2.3]

Fixed:

• Fixed memory issue with vcfanno in vep_somatic rule fixes #661

[7.2.2]

Fixed:

• An error with Sentieon for better management of memory fixes #621

[7.2.1]

Changed:

• Rename Github actions to reflect their content

[7.2.0]

Added:

• Changelog reminder workflow to Github
• Snakemake workflow for created PON reference
• Balsamic cli config command(pon) for creating json for PON analysis
• tumor lod option for passing tnscope-umi final variants
• Git guide to make balsamic release in FAQ docs

Changed:

• Expanded multiqc result search dir to whole analysis dir
• Simple test for docker container

Fixed:

• Correctly version bump for Dockerfile

Removed:

• Removed unused Dockerfile releases
• Removed redundant genome version from reference.json

[7.1.10]

Fixed:

• Bug in ngs_filter rule set for tumor-only WGS
• Missing delivery of tumor only WGS filter

[7.1.9]

Changed:

• only pass variants are not part of delivery anymore
• delivery tag file ids are properly matched with sample_name
• tabix updated to 0.2.6
• fastp updated to 0.20.1
• samtools updated to 1.12
• bedtools updated to 2.30.0

Removed:

• sentieon-dedup rule from delivery
• Removed all pre filter pass from delivery

[7.1.8]

Fixed:

• Target coverage (Picard HsMetrics) for UMI files is now correctly calculated.

Changed:

• TNscope calculated AF values are fetched and written to AFtable.txt.

[7.1.7]

Added:

• ngs_filter_tnscope is also part of deliveries now

Changed:

• rankscore is now a research tag instead of clinical
• Some typo and fixes in the coverage and constant metrics
• Delivery process is more verbose

Fixed:

• CNVKit output is now properly imported in the deliveries and workflow

[7.1.6]

Fixed:

• CSS style for qc coverage report is changed to landscape

[7.1.5]

Changed:

• update download url for 1000genome WGS sites from ftp to http

[7.1.4]

Changed:

• bump picard to version 2.25.0

[7.1.3]

Fixed:

• assets path is now added to bind path

[7.1.2]

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.
• Documentation autobuild on RTFD

[7.1.1]

Fixed:

• Moved all requirements to setup.py, and added all package_data there. Clean up unused files.

[7.1.0]

Removed

• tnsnv removed from WGS analysis, both tumor-only and tumor-normal
• GATK-BaseRecalibrator is removed from all workflows

Fixed

• 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

• All variant calling rules use proper tumor.merged.bam or normal.merged.bam as inputs

[7.0.2]

Added

• Updated docs with FAQ for UMI workflow

Fixed

• fix job scheduling bug for benchmarking
• rankscore's output is now a proper vcf.gz file
• Manta rules now properly make a sample_name file

[7.0.1]

Added

• github action workflow to autobuild release containers

[7.0.0]

Added

• balsamic init to download reference and related containers done in PRs #464 #538
• balsamic config case now only take a cache path instead of container and reference #538
• UMI workflow added to main workflow in series of PRs #469 #477 #483 #498 #503 #514 #517
• DRAGEN for WGS applications in PR #488
• A framework for QC check PR #401
• --quiet` option for run analysis PR #491
• Benchmark SLURM jobs after the analysis is finished PR #534
• One container per conda environment (i.e. decouple containers) PR #511 #525 #522
• --disable-variant-caller command for report deliver PR #439
• Added genmod and rankscore in series of two PRs #531 and #533
• Variant filtering to Tumor-Normal in PR #534
• Split SNV/InDels and SVs from TNScope variant caller PR #540
• WGS Tumor only variant filters added in PR #548

Changed

• Update Manta to 1.6.0 PR #470
• 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
• 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
• QoL changes to scheduler script PR #491
• QoL changes to how temporary directories are handlded PR #516
• TNScope model apply rule merged with TNScope variant calling for tumor-normal in WGS #540
• Decoupled fastp rule into two rules to make it possible to use it for UMI runs #570

Fixed

• A bug in Manta variant calling rules that didn't name samples properly to TUMOR/NORMAL in the VCF file #572

[6.1.2]

Changed

• Changed hk delivery tag for coverage-qc-report

[6.1.1]

Fixed

• No UMI trimming for WGS applications #486
• Fixed a bug where BALSAMIC was checking for sacct/jobid file in local mode PR #497
• readlink command in vep_germline, vep_somatic, split_bed, and GATK_popVCF #533
• Fix various bugs for memory handling of Picardtools and its executable in PR #534
• Fixed various issues with gsutils in PR #550

Removed

• gatk-register command removed from installing GATK PR #496

[6.1.1]

• Fixed a bug with missing QC templates after pip install

[6.1.0]

Added

• CLI option to expand report generation for TGA and WES runs. Please see balsamic report deliver --help
• BALSAMIC now generates a custom HTML report for TGA and WES cases.

[6.0.4]

Changed

• Reduces MQ cutoff from 50 to 40 to only remove obvious artifacts PR #535
• Reduces AF cutoff from 0.02 to 0.01 PR #535

[6.0.3]

Added

• config case subcommand now has --tumor-sample-name and --normal-sample-name

Fixed

• Manta resource allocation is now properly set PR #523
• VarDict resource allocation in cluster.json increased (both core and time allocation) PR #523
• minimum memory request for GATK mutect2 and haplotypecaller is removed and max memory increased PR #523

[6.0.2]

Added

• Document for Snakemake rule grammar PR #489

Fixed

• removed gatk3-register command from Dockerfile(s) PR #508

[6.0.1]

Added

• A secondary path for latest jobids submitted to cluster (slurm and qsub) PR #465

[6.0.0]

Added

• UMI workflow using Sentieon tools. Analysis run available via balsamic run analysis --help command. PR #359
• VCFutils to create VCF from flat text file. This is for internal purpose to generate validation VCF. PR #349
• Download option for hg38 (not validated) PR #407
• Option to disable variant callers for WES runs. PR #417

Fixed

• Missing cyvcf2 dependency, and changed conda environment for base environment PR #413
• Missing numpy dependency PR #426

Changed

• COSMIC db for hg19 updated to v90 PR #407
• Fastp trimming is now a two-pass trimming and adapter trimming is always enabled. This might affect coverage slightly PR #422
• All containers start with a clean environment #425
• All Sentieon environment variables are now added to config when workflow executes #425
• Branching model will be changed to gitflow

[5.1.0]

Fixed

• Vardict-java version fixed. This is due to bad dependency and releases available on conda. Anaconda is not yet update with vardict 1.8, but vardict-java 1.8 is there. This causes various random breaks with Vardict's TSV output. #403

Changed

• Refactored Docker files a bit, preparation for decoupling #403

Removed

• In preparation for GATK4, IndelRealigner is removed #404

[5.0.1]

Added

• Temp directory for various rules and workflow wide temp directory #396

Changed

• Refactored tags for housekeeper delivery to make them unique #395
• Increased core requirements for mutect2 #396
• GATK3.8 related utils run via jar file instead of gatk3 #396

[5.0.0]

Added

• Config.json and DAG draph included in Housekeeper report #372
• New output names added to cnvkit_single and cnvkit_paired #372
• New output names added to vep.rule #372
• Delivery option to CLI and what to delivery with delivery params in rules that are needed to be delivered #376
• Reference data model with validation #371
• Added container path to install script #388

Changed

• Delivery file format simplified #376
• VEP rules have "all" and "pass" as output #376
• Downloaded reference structure changed #371
• genome/refseq.flat renamed to genome/refGene.flat #371
• reverted CNVKit to version 0.9.4 #390

Fixed

• Missing pygments to requirements.txt to fix travis CI #364
• Wildcard resolve for deliveries of vep_germline #374
• Missing index file from deliverables #383
• Ambiguous deliveries in vep_somatic and ngs_filters #387
• Updated documentation to match with installation #391

Removed

• Temp files removed from list of outputs in vep.rule #372
• samtools.rule and merged it with bwa_mem #375

[4.5.0]

Added

• Models to build config case JSON. The models and descriptions of their contents can now be found in BALSAMIC/utils/models.py
• Added analysis_type to report deliver command
• Added report and delivery capability to Alignment workflow
• run_validate.sh now has -d to handle path to analysis_dir (for internal use only) #361

Changed

• Fastq files are no longer being copied as part of creation of the case config file. A symlink is now created at the destination path instead
• Config structure is no longer contained in a collestion of JSON files. The config models are now built using Pydantic and are contained in BALSAMIC/utils/models.py

Removed

• Removed command line option "--fastq-prefix" from config case command
• Removed command line option "--config-path" from config case command. The config is now always saved with default name "case_id.json"
• Removed command line option "--overwrite-config" from config-case command The command is now always executed with "--overwrite-config True" behavior

Refactored

• Refactored BALSAMIC/commands/config/case.py: Utility functions are moved to BALSAMIC/utils/cli.py Models for config fields can be found at BALSAMIC/utils/models.py Context aborts and logging now contained in pilot function Tests created to support new architecture
• Reduce analysis directory's storage

Fixed

• Report generation warnings supressed by adding workdirectory
• Missing tag name for germline annotated calls #356
• Bind path is not added as None if analysis type is wgs #357
• Changes vardict to vardict-java #361

[4.4.0]

Added

• pydantic to validate various models namely variant caller filters

Changed

• Variant caller filters moved into pydantic
• Install script and setup.py
• refactored install script with more log output and added a conda env suffix option
• refactored docker container and decoupled various parts of the workflow

[4.3.0]

Added

• Added cram files for targeted sequencing runs fixes #286
• Added mosdepth to calculate coverage for whole exome and targeted sequencing
• Filter models added for tumor-only mode
• Enabling adapter trim enables pe adapter trim option for fastp
• Annotate germline variant calls
• Baitset name to picard hsmetrics

Deprecated

• Sambamba coverage and rules will be deprecated

Fixed

• Fixed latest tag in install script
• Fixed lack of naming final annotated VCF TUMOR/NORMAL

Changed

• Increased run time for various slurm jobs fixes #314
• Enabled SV calls for VarDict tumor-only
• Updated ensembl-vep to v100.2

[4.2.4]

Fixed

• Fixed sort issue with bedfiles after 100 slop

[4.2.3]

Added

• Added Docker container definition for release and bumpversion

Changed

• Quality of life change to rtfd docs

Fixed

• Fix Docker container with faulty git checkout

[4.2.2]

Added

• Add "SENTIEON_TMPDIR" to wgs workflow

[4.2.1]

Changed

• Add docker container pull for correct version of install script

[4.2.0]

Added

• CNV output as VCF
• Vep output for PASSed variants
• Report command with status and delivery subcommands

Changed

• Bed files are slopped 100bp for variant calling fix #262
• Disable vcfmerge
• Picard markduplicate output moved from log to output
• Vep upgraded to 99.1
• Removed SVs from vardict
• Refactored delivery plugins to produce a file with list of output files from workflow
• Updated snakemake to 5.13

Fixed

• Fixed a bug where threads were not sent properly to rules

Removed

• Removed coverage annotation from mutect2
• Removed source deactivate from rules to suppress conda warning
• Removed plugins delivery subcommand
• Removed annotation for germline caller results

[4.1.0]

Added

• VEP now also produces a tab delimited file
• CNVkit rules output genemetrics and gene break file
• Added reference genome to be able to calculate AT/CG dropouts by Picard
• coverage plot plugin part of issue #75
• callable regions for CNV calling of tumor-only

Changed

• Increased time for indel realigner and base recalib rules
• decoupled vep stat from vep main rule
• changed qsub command to match UGE
• scout plugin updated

Fixed

• WGS qc rules - updated with correct options (picard - CollectMultipleMetrics, sentieon - CoverageMetrics)
• Log warning if WES workflow cannot find SENTIEON* env variables
• Fixes issue with cnvkit and WGS samples #268
• Fix #267 coverage issue with long deletions in vardict

[4.0.1] - 2019-11-08

Added

• dependencies for workflow report
• sentieon variant callers germline and somatic for wes cases

Changed

• housekeeper file path changed from basename to absolute
• scout template for sample location changed from delivery_report to scout
• rule names added to benchmark files

[4.0.0] - 2019-11-04

SGE qsub support release

Added

• install.sh now also downloads latest container
• Docker image for balsamic as part of ci
• Support for qsub alongside with slurm on run analysis --profile

Changed

• Documentation updated
• Test fastq data and test panel bed file with real but dummy data

[3.3.1] - 2019-10-28

Fixed

• Various links for reference genome is updated with working URL
• Config reference command now print correct output file

[3.3.0] - 2019-10-24

somatic vcfmerge release

Added

• QC metrics for WGS workflow
• refGene.txt download to reference.json and reference workflow
• A new conda environment within container
• A new base container built via Docker (centos7:miniconda3_4_6_14)
• VCFmerge package as VCF merge rule (https://github.com/hassanfa/VCFmerge)
• A container for develop branch
• Benchmark rules to variant callers

Changed

• SLURM resource allocation for various variancalling rules optimized
• mergetype rule updated and only accepts one single tumor instead of multiple

[3.2.3] - 2019-10-24

Fixed

• Removed unused output files from cnvkit which caused to fail on targetted analysis

[3.2.2] - 2019-10-23

Fixed

• Removed target file from cnvkit batch

[3.2.1] - 2019-10-23

Fixed

• CNVkit single missing reference file added

[3.2.0] - 2019-10-11

Adds:

• CNVkit to WGS workflow
• get_thread for runs

Changed:

• Optimized resources for SLURM jobs

Removed:

• Removed hsmetrics for non-mark duplicate bam files

[3.1.4] - 2019-10-08

Fixed

• Fixes a bug where missing capture kit bed file error for WGS cases

[3.1.3] - 2019-10-07

Fixed

• benchmark path bug issue #221

[3.1.2] - 2019-10-07

Fixed

• libreadline.so.6 symlinking and proper centos version for container

[3.1.1] - 2019-10-03

Fixed

• Proper tag retrieval for release ### Changed
• BALSAMIC container change to latest and version added to help line

[3.1.0] - 2019-10-03

TL;DR:

• QoL changes to WGS workflow
• Simplified installation by moving all tools to a container

Added

• Benchmarking using psutil
• ML variant calling for WGS
• --singularity option to config case and config reference

Fixed

• Fixed a bug with boolean values in analysis.json

Changed

• install.sh simplified and will be depricated
• Singularity container updated
• Common somatic and germline variant callers are put in single file
• Variant calling workflow and analysis config files merged together

Removed

• balsamic install is removed
• Conda environments for py36 and py27 are removed

[3.0.1] - 2019-09-11

Fixed

• Permissions on analysis/qc dir are 777 now

[3.0.0] - 2019-09-05

This is major release. TL;DR:

• Major changes to CLI. See documentation for updates.
• New additions to reference generation and reference config file generation and complete overhaul
• Major changes to reposityory structure, conda environments.

Added

• Creating and downloading reference files: balsamic config reference and balsamic run reference
• Container definitions for install and running BALSAMIC
• Bunch of tests, setup coveralls and travis.
• Added Mutliqc, fastp to rule utilities
• Create Housekeeper and Scout files after analysis completes
• Added Sentieon tumor-normal and tumor only workflows
• Added trimming option while creating workflow
• Added multiple tumor sample QC analysis
• Added pindle for indel variant calling
• Added Analysis finish file in the analysis directory

Fixed

• Multiple fixes to snakemake rules

Changed

• Running analysis through: balsamic run analysis
• Cluster account and email info added to balsamic run analysis
• umi workflow through --umi tag. [workflow still in evaluation]
• sample-id replaced by case-id
• Plan to remove FastQC as well

Removed

• balsamic config report and balsamic report
• sample.config and reference.json from config directory
• Removed cutadapt from workflows

[2.9.8] - 2019-01-01

Fixed

• picard hsmetrics now has 50000 cov max
• cnvkit single wildcard resolve bug fixed

[2.9.7] - 2019-02-28

Fixed

• Various fixes to umi_single mode
• analysis_finish file does not block reruns anymore
• Added missing single_umi to analysis workflow cli

Changed

• vardict in single mode has lower AF threshold filter (0.005 -> 0.001)

[2.9.6] - 2019-02-25

Fixed

• Reference to issue #141, fix for 3 other workflows
• CNVkit rule update for refflat file

[2.9.5] - 2019-02-25

Added

• An analysis finish file is generated with date and time inside (%Y-%M-%d T%T %:z)

[2.9.4] - 2019-02-13

Fixed

• picard version update to 2.18.11 github.com/hassanfa/picard

[2.9.3] - 2019-02-12

Fixed

• Mutect single mode table generation fix
• Vardict single mode MVL annotation fix

[2.9.2] - 2019-02-04

Added

• CNVkit single sample mode now in workflow
• MVL list from cheng et al. 2015 moved to assets

[2.9.1] - 2019-01-22

Added

• Simple table for somatic variant callers for single sample mode added

Fixed

• Fixes an issue with conda that unset variables threw an error issue #141

[2.9.0] - 2019-01-04

Changed

• Readme structure and example
• Mutect2's single sample output is similar to paired now
• cli path structure update

Added

• test data and sample inputs
• A dag PDF will be generated when config is made
• umi specific variant calling

[2.8.1] - 2018-11-28

Fixed

• VEP's perl module errors
• CoverageRep.R now properly takes protein_coding transcatipts only

[2.8.0] - 2018-11-23

UMI single sample align and QC

Added

• Added rules and workflows for UMI analysis: QC and alignment

[2.7.4] - 2018-11-23

Germline single sample

Added

• Germline single sample addition ### Changed
• Minor fixes to some rules to make them compatible with tumor mode

[2.7.3] - 2018-11-20

Fixed

• Various bugs with DAG to keep popvcf and splitbed depending on merge bam file
• install script script fixed and help added

[2.7.2] - 2018-11-15

Changed

• Vardict, Strelka, and Manta separated from GATK best practice pipeline

[2.7.1] - 2018-11-13

Fixed

• minro bugs with strelka_germline and freebayes merge ### Changed
• removed ERC from haplotypecaller

[2.7.0] - 2018-11-08

Germline patch

Added

• Germline caller tested and added to the paired analysis workflow: Freebayes, HaplotypeCaller, Strelka, Manta

Changed

• Analysis config files updated
• Output directory structure changed
• vep rule is now a single rule
• Bunch of rule names updated and shortened, specifically in Picard and GATK
• Variant caller rules are all updated and changed
• output vcf file names are now more sensible: {SNV,SV}.{somatic,germline}.sampleId.variantCaller.vcf.gz
• Job limit increased to 300

Removed

• removed bcftools.rule for var id annotation

Changed

Fixed

[2.6.3] - 2018-11-01

Changed

• Ugly and godforsaken runSbatch.py is now dumping sacct files with job IDs. Yikes!

[2.6.2] - 2018-10-31

Fixed

• added --fastq-prefix option for config sample to set fastq prefix name. Linking is not changed.

[2.6.1] - 2018-10-29

Fixed

• patched a bug for copying results for strelka and manta which was introduced in 2.5.0

[2.5.0] - 2018-10-22

Changed

• variant_panel changed to capture_kit
• sample config file takes balsamic version
• bioinfo tool config moved bioinfotool to cli_utils from config report

Added

• bioinfo tool versions is now added to analysis config file

[2.4.0] - 2018-10-22

Changed

• balsamic run has 3 stop points: paired variant calling, single mode variant calling, and QC/Alignment mode.
• balsamic run [OPTIONS] -S ... is depricated, but it supersedes analysis_type mode if provided.

[2.3.3] - 2018-10-22

Added

• CSV output for variants in each variant caller based on variant filters
• DAG image of workflow ### Changed
• Input for variant filter has a default value
• delivery_report is no created during config generation
• Variant reporter R script cmd updated in balsamic report

[2.3.2] - 2018-10-19

Changed

• Fastq files are now always linked to fastq directory within the analysis directory

Added

• balsamic config sample now accepts individual files and paths. See README for usage.

[2.3.1] - 2018-09-25

Added

• CollectHSmetric now run twice for before and after markduplicate

[2.3.0] - 2018-09-25

Changed

• Sample config file now includes a list of chromosomes in the panel bed file

Fixed

• Non-matching chrom won't break the splitbed rule anymore
• collectqc rules now properly parse tab delimited metric files

[2.2.0] - 2018-09-11

Added

• Coverage plot to report
• target coverage file to report json
• post-cutadapt fastqc to collectqc
• A header to report pdf
• list of bioinfo tools used in the analysis added to report ### Changed
• VariantRep.R now accepts multiple inputs for each parameter (see help)
• AF values for MSKIMPACT config ### Fixed
• Output figure for coverageplot is now fully square :-)

[2.1.0] - 2018-09-11

Added

• normalized coverage plot script
• fastq file IO check for config creation
• added qos option to balsamic run ### Fixed
• Sambamba depth coverage parameters
• bug with picard markduplicate flag

[2.0.2] - 2018-09-11

Added

• Added qos option for setting qos to run jobs with a default value of low

[2.0.1] - 2018-09-10

Fixed

• Fixed package dependencies with vep and installation

[2.0.0] - 2018-09-05

Variant reporter patch and cli update

Added

• Added balsamic config sample and balsamic config report to generate run analysis and reporting config
• Added VariantRep.R script to information from merged variant table: variant summry, TMB, and much more
• Added a workflow for single sample mode alignment and QC only
• Added QC skimming script to qccollect to generate nicely formatted information from picard ### Changed
• Change to CLI for running and creating config
• Major overhaul to coverage report script. It's now simpler and more readable! ### Fixed
• Fixed sambamba depth to include mapping quality
• Markduplicate now is now by default on marking mode, and will NOT remove duplicates
• Minor formatting and script beautification happened

[1.13.1] - 2018-08-17

Fixed

• fixed a typo in MSKMVL config
• fixed a bug in strelka_simple for correct column orders

[1.13.0] - 2018-08-10

Added

• rule for all three variant callers for paired analysis now generate a simple VCF file
• rule for all three variant callers for paired analysis to convert VCF into table format
• MVL config file and MVL annotation to VCF calls for SNV/INDEL callers
• CALLER annotation added to SNV/INDEL callers
• exome specific option for strelka paired
• create_config subcommand is now more granular, it accepts all enteries from sample.json as commandline arguments
• Added tabQuery to the assets as a tool to query the tabulated output of summarized VCF
• Added MQ annotation field to Mutect2 output see #67 ### Changed
• Leaner VCF output from mutect2 with coverage and MQ annotation according to #64
• variant ids are now updated from simple VCF file ### Fixed
• Fixed a bug with sambamba depth coverage reporting wrong exon and panel coverage see #68
• The json output is now properly formatted using yapf
• Strelka rule doesn't filter out PASS variants anymore fixes issue #63

[1.12.0] - 2018-07-06

Coverage report patch

Added

• Added a new script to retrieve coverage report for a list of gene(s) and transcripts(s)
• Added sambamba exon depth rule for coverage report
• Added a new entry in reference json for exon bed file, this file generated using: https://github.com/hassanfa/GFFtoolkit ### Changed
• sambamba_depth rule changed to sambama_panel_depth
• sambamba depth now has fix-mate-overlaps parameter enabled
• sambamba string filter changed to unmapped or mate\_is\_unmapped) and not duplicate and not failed\_quality\_control.
• sambamba depth for both panel and exon work on picard flag (rmdup or mrkdup). ### Fixed
• Fixed sambamba panel depth rule for redundant coverage parameter

[1.11.0] - 2018-07-05

create config patch for single and paired mode

Changed

• create_config is now accepting a paired|single mode instead of analysis json template (see help for changes). It is not backward compatible ### Added
• analysis_{paired single}.json for creating config. Analysis.json is now obsolete. ### Fixed
• A bug with writing output for analysis config, and creating the path if it doesn't exist.
• A bug with manta rule to correctly set output files in config.
• A bug that strelka was still included in sample analysis.

[1.10.0] - 2018-06-07

Added

• Markduplicate flag to analysis config

[1.9.0] - 2018-06-04

Added

• Single mode for vardict, manta, and mutect.
• merge type for tumor only ### Changed
• Single mode variant calling now has all variant calling rules ### Fixed
• run_analaysis now accepts workflows for testing pyrposes

[1.8.0] - 2018-06-01

Changed

• picard create bed interval rule moved into collect hsmetric
• split bed is dependent on bam merge rule
• vardict env now has specific build rather than URL download (conda doesn't support URLs anymore) ### Fixed
• new logs and scripts dirs are not re-created if they are empty

[1.7.0] - 2018-05-31

Added

• A source altered picard to generated more quality metrics output is added to installation and rules

[1.6.0] - 2018-05-30

Added

• report subcommand for generating a pdf report from a json input file
• Added fastqc after removing adapter ### Changed
• Markduplicate now has both REMOVE and MARK (rmdup vs mrkdup)
• CollectHSMetrics now has more steps on PCT_TARGET_BASES

[1.5.0] - 2018-05-28

Changed

• New log and script directories are now created for each re-run ### Fixed
• Picardtools' memory issue addressed for large samples

[1.4.0] - 2018-05-18

Added

• single sample analysis mode
• alignment and insert size metrics are added to the workflow ### Changed
• collectqc and contest have their own rule for paired (tumor vs normal) and single (tumor only) sample.

[1.3.0] - 2018-05-13

Added

• bed file for panel analysis is now mandatory to create analaysis config

[1.2.3] - 2018-05-13

Changed

• vep execution path
• working directory for snakemake

[1.2.2] - 2018-05-04

Added

• sbatch submitter and cluster config now has an mail field ### Changed
• create_config now only requires sample and output json. The rest are optional

[1.2.0] - 2018-05-02

Added

• snakefile and cluster config in run analysis are now optional with a default value

[1.1.2] - 2018-04-27

Fixed

• vardict installation was failing without conda-forge channel
• gatk installation was failing without correct jar file

[1.1.1] - 2018-04-27

Fixed

• gatk-register tmp directory

[1.1.0] - 2018-04-26

Added

• create config sub command added as a new feature to create input config file
• templates to generate a config file for analysis added
• code style template for YAPF input created. see: https://github.com/google/yapf
• vt conda env added

Changed

• install script changed to create an output config
• README updated with usage

Fixed

• fastq location for analysis config is now fixed
• lambda rules removed from cutadapt and fastq

[1.0.3-rc2] - 2018-04-18

Added

• Added sbatch submitter to handle it outside snakemake ### Changed
• sample config file structure changed
• coding styles updated

[1.0.2-rc2] - 2018-04-17

Added

• Added vt environment ### Fixed
• conda envs are now have D prefix instead of P (develop vs production)
• install_conda subcommand now accepts a proper conda prefix

[1.0.1-rc2] - 2018-04-16

Fixed

• snakemake rules are now externally linked

[1.0.0-rc2] - 2018-04-16

Added

• run_analysis subcommand
• Mutational Signature R script with CLI
• unittest to install_conda
• a method to semi-dynamically retrieve suitable conda env for each rule

Fixed

• install.sh updated with gatk and proper log output
• conda environments updated
• vardict now has its own environment and it should not raise anymore errors

[1.0.0-rc1] - 2018-04-05

Added

• install.sh to install balsamic
• balsamic barebone cli
• subcommand to install required environments
• README.md updated with basic installation instructions

Fixed

• conda environment yaml files