v1.9.1

Bugfix related to how some external tools were being called

v1.9.0

New:

• add --unpairedOutFastqto taxon_filter.py trim_trimmomatic: two optional parameters for specifying paths to fastq files containing Trimmomatic’s unpaired reads. If the parameters are not specified, the unpaired reads are written to temp and discarded.
• optional intrahost params are now exposed in the Snakemake config.yaml file:
  • intrahost.py vphaser_one_sample --minReadsEach and --maxBias
  • intrahost.py merge_to_vcf --naive_filter
• The plot_coverage function now accepts --plotOnlyNonDuplicates that only includes reads not marked with a 1024 bitmask.
• The align_and_plot_coverage function now accepts --excludeDuplicates, which performs Picard’s MarkDuplicates on the aligned bam, and then calls plot_coverage with --plotOnlyNonDuplicates. Other parameters are added to change the JVMmemory and pass opts to Picard.
• Novoalign parameter strings for the Snakemake rules refine_assembly_1, refine_assembly_2, and map_reads_to_self have been exposed in the config.yaml file
• Downsampling before de novo assembly is now performed in bam space via Picard's DownsampleSam. This is faster and allows unpaired reads to be included in cases where the paired read count is below the Trinity input size threshold.

Fixed:

• Fix Trimmomatic usage bug: explicitly use Phred-33 quality scores. See PR #409 for more information.
• Memory limit raised for lastal rule (3->8G), and Snakemake merge_one_per_sample rule (7->10G) to suit larger project sizes
• For Broad users, the Snakemake rule filter_to_taxon is set to use the long UGER queue

Updated:

• Picard updated, v1.126 -> v1.141

v1.8.0

New features:

• reports.py plot_coverage — creates a coverage plot for a mapped .bam file. Multiple chart styles are supported, and data can be drawn as a line, filled line, or point series
• reports.py align_and_plot_coverage — performs a quick BWA alignment between an unmapped bam file and a reference .fasta file, and then creates a coverage plot via reports.py plot_coverage.

Example chart:

v1.7.1

Fixes:

• easy deploy script has been updated in a few more places to reflect shift to conda-based environment
• the pipeline run-pipe.sh and jobscript.shscripts now use the conda environment
• the easy deploy script now uses miniconda's python3, rather than setting the version based on the system python

v1.7.0

New:

• add parser_bwamem_idxstats, which takes reads, aligns to reference with BWA-MEM and performs samtools idxstats

Updates:

• easy-deploy now uses own conda install (fix)
• samtools sort is now multithreaded (improved performance)
• bam->fastq conversions now use Samtools rather than Picard (improved performance)
• Update samtools to 1.3.1
• --commonBarcodes is now specified by default in illumina_demux call in Snakemake demux.rules
• more robust handling of barcode files with extraneous end-of-line spaces

v1.6.1

Updates:

• make easy-deploy script more generic (less Broad specific)
• more documentation updates
• bugfixes to snakemake rules
• add more forgiveness in pre-Trinity filtration steps (duplicate removal, unpaired read removal) when read counts are below subsampling threshold.

In particular, the last set of changes will increase the success rate of de novo assembly when viral genomes are degraded or have small fragment / segment sizes and have adapter read through issues in the second read.

v1.6.0

New:

• added common_barcodes command to illumina.py to write a report of the barcodes present in a run, sorted in descending order by count
• added --commonBarcodes to illumina_demux command to write a common barcodes file as part of the demultiplexing process

Fixes:

• more robust handling of sample sheet data
• Snakemake pipeline fixes related to how Snakemake handles parameters in newer versions
• update trimmomatic to 0.36
• trimmomatic install fix
• various fixes in interhost.rules (Snakemake pipeline)

v1.5.5

Small fixes

• OSX compatibility fixes (most steps should work, with the exception of intrahost and metagenomics)
• sample name sanitization in demux
• some snakemake pipeline fixes

v1.5.4

Relaxes Trimmomatic defaults (pre-trinity filters) and exposes a few Trimmomatic options, adds a new field to intrahost VCF output, and improvements and updates to Travis CI setup and tool install process.

Details:

• Trimmomatic leading/trailing Q cutoff values have been lowered to a default score of 15. These values, as well as the sliding window size, cutoff, and minlength have been exposed as argparse parameters.
• Add the 'DP' field to the VCF file created at the end of the intrahost component of the pipeline. The field gives, at
  each position, the read depth for each sample.
• Append resource usage to UGER logs
• Remove a lot of non-conda-based fallback tool installers
• Remove Travis caching of conda-installed tools. Also keeps coveralls test coverage consistent.
• Add standalone install_tools.py script that installs tools w/o the need for requirements-tests.txt
• Remove pytest.ini and move into Travis-specific env variables so that developers can specify their own options appropriate to their local dev environment.
• Run flake8 only on pull requests and master branch (skip branch commits)
• Add a requirements-conda.txt file that can be used with conda create to optimize/speed up tool installation

v1.5.3

• fix Tool._patch, which fixes Krona installation