[16.0.0]

Added:

MSIsensor-pro container #1444
MSI analysis to the tumor-normal workflow #1454
Sentieon install directory path to case config arguments #1461
QC threshold for lymphoma_MRD panel #1479
MSI tumor-normal analysis to housekeeper storage #1483
UMI extraction and deduplication to TGA workflow #1358
GENS input files for TGA #1448
Padding of bed-regions for CNVkit to minimum 100 bases #1469
Added min mapq 20 to CNVkit PON workflow #1465
CNVkit PONs for Exome comprehensive 10.2, GMSsolid 15.2, GMCKsolid 4.2 #1465
Merged VarDict with TNscope in all TGA workflows #1475
New filter for VarDict for tumor in normal contamination #1475
Export TMP environment variables to rules that lack them #1475
Added genmod ranked VCFs to be delivered #1475
Added family-id to genmod in order to get ranked variants to Scout #1475
Added Raw TNscope calls and unfiltered research-annotated SNVs to delivery #1475
Argument for SNV Artefact LoqusDB to all workflows #1481
TNscope tag to variant info-field for TGA workflow #1497

Changed:

Cluster scheduler script for immediate submit #1372
SLEEP_BEFORE_START to 600s #1372
Updated Multiqc to version 1.22.3 #1441
Upgrade vcf2cytosure version to 0.9.1 and remove hardcoded versions #1456
Create new PONs for GMCKSolid v4.1, GMSMyeloid v5.3, and GMSlymphoid v7.3 #1465
Refactored CNVkit rules #1465
Refactored BCFtools filter rules #1475
Renamed final UMI bamfile to ensure hsmetrics is picked up by multiqc #1475
Changed ranking model VCF from research to clinical #1475
Lowered minimum AF for TGA from 0.007 to 0.005 #1475
Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 #1475
Fixed TNscope research VCF filters to either PASS or triallelic site #1475
Increased maximal amount of redirects for lychee test following links in docs to 10 #1488
Updated readthedocs tools versions #1489
Renamed UMI consensusfiltered bamfile to be picked up by multiqc #1490

Removed:

GATK3 #1432
gatk_contest rule #1432
SGE (qsub) support #1372
Fastq quality and UMI trimming command-line options #1358
ML model for TNscope #1475
All code associated with TNhaplotyper #1475
Removed research.filtered.pass files from delivery #1475
Removed VarDict germline filter, replaced by relative normal af / tumor af filter #1497

Fixed:

Corrected tool name in deduplication metrics #1441
MSI table #1459
Pin numpy version in CNVkit container #1457
CNVkit incorrect version in the documentation #1457
MSIsensor-pro container and updated msisensor to version 1.3.0 #1486
Somalier container and updated somalier to version 0.2.19 #1487
Vardict memory and tmpdir allocation #1492
Vardict tumor only allocates dynamic number of cores #1495

[15.0.1]

Added:

CLI option for the minimum raw reads supporting each UMI group filter

[15.0.0]

Added:

high_normal_tumor_af_frac filter in bcftools for TNscope T+N filtering out more than 30% TINC #1289
New option for exome samples --exome with modified bcftools filters compared to standard targeted workflow #1414
Custom samtools script for the detection of IGH::DUX4 rearrangements #1397

Changed:

Reduced stringency of minimum MQ for all TGA to 30 from 40 #1414
Removed -u flag from VarDict T+N and T only rules to remove calling only in reverse reads of overlapping mates #1414
Removed -U flag to VarDict T+N rule to start calling SVs #1414

Removed:

alt_allele_in_normal filter from TNscope T+N workflows #1289

Fixed:

initial filter keeping only PASS or triallelic-site from T+N bcftools quality filter rule has been removed #1424

[14.0.1]

Fixed:

PureCN fail due to bash strict mode #1406
Corrected name of CNVkit container in the CNVkit PON creation workflow #1412

[14.0.0]

Added:

bcftools filters for PR:SR evidence in Manta calls #1371
--exome argument to Manta runs in TGA cases #1371
MultiQC intermediate files to deliverables #1388

Removed:

Extra bcftools filters that allows MaxDepth filtered variants in the final SV VCF #1371
Unused arguments from delivery.py #1388

Fixed:

ASCAT-Ngs container #1395
bcftools in manta_tumor_normal uses correct column for tumor read filtering #1400

[13.0.1]

Added:

Sleep rule before start to fix key_error #1311

Fixed:

Missing __init__.py in snakemake_rules folders #1383

[13.0.0]

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 #1232
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
GATK container #1266
Resolved FASTQ paths to sample dictionary (balsamic logging) #1275
Picard HsMetrics and CollectGcBiasMetrics for WGS #1288
LOH to TGA workflow #1278
CNVs from PureCN to TGA workflow #1278
Command-line arguments and rules for creation of GENS files #1279
Somatic and germline Loqusdb annotation to ReadtheDocs #1317
Postprocess step before VarDict in TGA #1332
CNV report for TGA workflow #1339
wkhtmltopdf to system requirements #1339
Store WGS CNV report plots #1347

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 Metrics models to pydantic v2 #1270
Migrate Snakemake models to pydantic v2 #1268
Migrate Cache models to pydantic v2 #1274
Made BALSAMIC compatible with multiple PON creation workflows #1279
Use StrEnum from python enum #1303
Renamed final cram bamfile to format <tumor/normal>.<LIMS_ID>.cram #1307
Updated snakemake version to 7.32.4 #1308
Migrate analysis models to pydantic v2 #1306
Split analysis model into config and params models #1306
Renamed name in sample column of final clincial vcfs #1310
Update Gens HK tags #1319
Increased memory and threads for VarDict #1332
Updated ReadtheDocs with GENS and structural pipeline changes #1327
Migrate WGS CNV report generation to pypdf & pdfkit #1346

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
QC workflow store #1295
MultiQC rule missing input files #1321
gens_preprocessing rule missing python directive #1322
CADD annotations container path and code smells #1323
Sonarcloud reported issues #1348
Loqusdb SV annotation somatic fields #1354

Removed:

Config folder #1175
Quality trimming of fastqs for UMI workflow #1176
Balsamic container #1230
Plugin CLI #1245
Realignment step for TGA workflow #1272
Archived/outdated workflows and scripts #1296
Sed command to convert CNVpytor integer to float, deprecated by updated CNVpytor version #1310
Removed max AF 1 filter from bcftools #1338
Extra samtools sort command from WGS cases #1334

[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

Files

CHANGELOG.rst

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CHANGELOG.rst

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