CHANGELOG

[X.X.X]

Removed

  • tnsnv removed from WGS analysis, both tumor-only and tumor-normal

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