Duplex-Seq-Pipeline v2.1.4

Bugfix:
Fix Gene sums bug in MutationFreqFromVCF.py

Duplex-Seq-Pipeline v2.1.3

v2.1.3:
Bugfix:
Add additional checks to the 'sample' column of the config file, to exclude characters that aren't allowed in file names.

Duplex-Seq-Pipeline v2.1.2

v2.1.2:
Bugfix:
Re-add pre variant calling checkpoint to fix non-functionality of rerun mode 1.
Remove "ancient" keyword and snakemake version restriction to fix run problems on macOS X
Fix issue in VCF generation where the same variant could appear multiple times

Internal Changes:
Instead of removing families containing Ns or mononucleotide repeats in UMIs after all consensus making happened, do it before any consensus making hapens. The tagstats output removes unchanged at this time; the only difference will be in the SSCS output, which will not contain reads with UMIs that contain Ns or mononucleotide repeats (it did previously).
Track number of N-containing UMIs in CM_stats file.
Modify rerun to check for file existance (depends on OS module from Python standard library; may not work identically on all systems).

v2.1.1:
Bugfix:
Fix issue where masking in countmuts file was not applied correctly

Duplex-Seq-Pipeline v2.1.0

v2.1.0:

This version contains a couple of modifications to make debugging easier. It shouldn't result in any changes in the output as compared to v2.0.1, just make debugging issues that may arise easier.

Bugfix:
Fix spelling on some rule names
New Features:
Populate log files, add missing log files, and normalize log file names
Add '--keep-going' to snakemake command in run script, which allows for
the pipeline to continue to run independent steps if one step fails;
rerun setup script to take advantage of this.

Duplex-Seq-Pipeline v2.0.1

Bugfix release: pipeline crashed when a masking bed file was provided.

Duplex-Seq-Pipeline v2.0.0

V2.0.0 of the Duplex-Seq-Pipeline is here! Included is a new variant caller (VarDict), a move away from GATK, a consequent simplified setup, and improved setup time using Mamba. Use of this version will require extra dependencies not needed for v1.1.X (particularly Mamba), re-running environment setup, re-building of your BLAST database, and a few config file changes. In addition, if you have custom recovery scripts, those will need to be re-written to conform to a new format.

Bugfixes:
Add definition of negative taxIDs to report.
Fix bed blocks issue where terminal comma would cause crashes
Fix table formatting for countmuts and depth tables in report
Change clustering to avoid using SNPs for clustering analysis.
explicitly convert report to HTML
Fix fastq output third line from consensusMaker
Set quality of N bases from consensusMaker to 0
Fix crash on non-CATG bases in the reference genome

New Features:
Change recovery script format
Create new test data set that can better demonstrate the BLAST filter
Create new test reference / blastDB to match new test dataset
Add extra tests to the test config file
Make retrieveSummary.py work from the whole-pipeline config file
Reorganize BLAST control to make running without BLAST more explicit.
Add unlock script to setup script
Implement new depth script
Implement VarDict
Move the PostBlastRecovery to its own environment, allowing custom user programs without affecting the base environment.
Create script to summarize depth based on a provided bed file
Add the ability to select which filters the mutation frequency program applies.
Add % mapped raw read to the summary CSV
Add RawOnTarget to summaryCSV
Add masking functionality
Change countMutsPerCycle to allow filtering out mutations based on VCF filters, and to allow for filtering of near indel variants. Also allows for an "include" mode that includes only variants in the VCF file. Modify Snakefile to allow this method to draw from the countmuts filtering parameters.
Add adapter clipping
Add Mamba frontend to setup script.
Add readout for % on target SSCS and DCS to summaryCSV, report.

Internal Changes:
Add gitignore rule to ignore user-generated recovery scripts
Remove chrM_recovery, which is a custom recovery script from our lab
Remove testConfig.csv, since it is created by the setup script
Remove GATK3 from setup and Snakefile
Add vardict-java to environment
Modify MakeDepthPlot.R and retrieveSummary.py to point to new files.
Add VarDict-based Muts by Read Position program (not used)
Give final read length to MutsPerCycle, instead of initial read length.
Remove extra environment setup rules
Move BedParser to seperate file
Added pre-variant calling BAM filter to BED coordinates
Make prevar file temporary.
Add error checking to enforce number of blockStarts and blockSizes
add str and repr methods for Bed_Line
Add Bed_Writer functionality
Add DepthSummaryCsv to Snakefile
Add filter definitions to mutation frequency output and report
Verify that a variant is consists entirely of ACGTN bases
Change r versioning in DS_env_full
Add a bed buffering step pre-vardict
Add bedtools to run environment
Change BLAST database setup and application

Duplex-Seq-Pipeline v1.1.6

v1.1.6:
January 12, 2021
Bugfix:
Fix non-working non-unique mode for countmuts files

v1.1.5:
November 20, 2020
Bugfix:
Fix bug on line 375 with 0-position starts in bed files

Duplex-Seq-Pipeline v1.1.4

Fixes two bugs:

• Crash on 'N' ref bases in muts_per_cycle
• Explicitly convert report to html for compatibility with nbconvert 6.0.0+

Duplex-Seq-Pipeline v1.1.2

Fixes a few bugs:

• Misnamed defaults for maxClonal, maxClonal,
• Misnamed error checker for rgpl
• Fixed symlinking in clipBam step when no clipping is requested. (replace with copying)

Duplex-Seq-Pipeline v1.1.1

CHANGELOG

v1.1.1:

###Bugfix:

• SNPs VCF file wasn't being preserved. This fixes that issue.