CHANGELOG¶
[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 WGSMissing 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-normalGATK-BaseRecalibrator is removed from all workflows
Fixed¶
Fixed issue 577 with missing
tumor.merged.bam
andnormal.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
ornormal.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 #538balsamic config case
now only take a cache path instead of container and reference #538UMI 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 forrun analysis
PR #491Benchmark 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 forreport deliver
PR #439Added 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 invep_germline
,vep_somatic
,split_bed
, andGATK_popVCF
#533Fix 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
subcommandRemoved 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 containerDocker 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 toconfig case
andconfig reference
Fixed¶
Fixed a bug with boolean values in analysis.json
Changed¶
install.sh
simplified and will be depricatedSingularity 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 removedConda 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
andbalsamic 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 bycase-id
Plan to remove FastQC as well
Removed¶
balsamic config report
andbalsamic report
sample.config
andreference.json
from config directoryRemoved 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 forconfig 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 tocapture_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 supersedesanalysis_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 generationVariant 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
### FixedSambamba 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
andbalsamic config report
to generate run analysis and reporting configAdded
VariantRep.R
script to information from merged variant table: variant summry, TMB, and much moreAdded 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