CHANGELOG

metaWRAP v=1.4 (in development)
	Kraken
		added new module "kraken2" for running kraken2 instead of kraken1 for read or assembly classification

metaWRAP v=1.3 (August 2020)
	Assembly
		fixed typo where megahit was not using the specified tmp directory
	Annotate_bins
		removed manual perl library handling feature
	Quant_bins
		bin coverage is now estimated with weighted median coverage (reduces contribution of outliers)
		fixed warning message to pring to stderr
		allow for periods in sample names
		allow for all 0 columns or rows
	General
		enforce MKL build of blas software to prevent CONCOCT infinite warning messages
		return correct error code instead of always returning 0
	Binning
		added SAM file cleanup step
		fixed library dependancy causing endless OPEN blas warning when running CONCOCT
		fixed assembly truncation bug after interrupted binning run
		fixed bug that left trailing characters in contigs of concoct bins, leading to refinement problems later
	Bin_refinement
		added additional checkpoints to prevent re-running checkm if program terminated before completing
		algorithm now ignores bins smaller than 50Kbp or larger than 20Mbp to save time
	Blobology
		fixed perl path to #!/usr/bin/env perl in scripts
	Kraken
		fixed syntax bug where some systems would misinterpret comments at the end of lines


metaWRAP v=1.2 (April 2019)
	General
		config-metawrap sets database locations to $HOME by defualt during installation
		numpy, openblas, and scipy versions updated for concoct 1.0
		enforce CheckM v1.0.12 (newer versions are reported to fail)
		fixed depricated matplotlib functions in plotting scripts
		updated to Samtools v1.9 to avoid libcrypto.so.1.0.0 issues
		simplified metaWRAP preprequisite programs to base minimum number (but with strict version control)
	Assembly
		added "--restart-from last" feature for metaspades to allow continuation of previously terminated runs
	Read_qc
		added support for non-human host contamination removal with bmtagger
	Bin_refinement
		set_axis_bgcolor was replaced by set_facecolor in plotting function
		the module is able to continue previous progress is the .stats files are present
		matplotlib depricated option fixes
	Reassemble_bins
		set_axis_bgcolor was replaced by set_facecolor in plotting function
		added check limit on maximum number of open python file handles
	Binning
		fixed syntax bug coming from comment lines following "next line" character
		split the alignment and alignment sorting stages to help resolve stalled jobs
		matplotlib depricated option fixes
		added support for CONCOCT v1.0, improving binning performance
		added recommended contig splitting step for CONCOCT, improving its performance on larger contigs
		CONCOCT now supports multi-threading greatly speeding up binning on larger data
		fixed outdated path handling in new CONCOCT implementation
		updated to maxbin2 v2.2.6
	Blobology
		removed shuffle reads features
		use paired reads for bowtie alignment
		split alignment and BAM conversions steps to clarity and debugging
	Classify_bins
		added exception to prune hits script to account for newer version of NCBI database
	Kraken
		kraken now pre-loads the database before running by default, improving speed on systems with slow IO
		added --no-preload option for running form hard disk for lower memory requirements
		fixed exception that crashed the module if kraken-translate could not find a taxonomy for a classification
	Quant_bins
		utilize the --meta option for salmon
		utilize the -p option to enable multi-threading


metaWRAP v=1.1 (January 2019)
	General
		modified conda requirements for software version (multiple)
		added perl-lwp-simple as a dependancy for MaxBin2
		clarifying notes in many help messages
		changed python script shebangs to force use python2.7
		deleted depricated modules "all" and "phylosift", to avoid confusion
		main help message now displays metawrap version
	Binning
		removed insert size calculations to avoid stalled bwa run bug
		added proper scikit dependancy to avoid GMM errors when running CONCOCT
		fixed Maxbin distribution to use conda's Perl instead of system Perl (in maxbin v=2.2.5)
		fixed checkm folder error when resuming a previously attempted run
		changed default MaxBin2 marker set to the Bacterial marker set
		added --universal option to set MaxBin2 to use the universal marker genes for improved Archaea binning 
		added -l option that sets the minimum contig length to bin for all four binners
		removed cleanup feature so re-running the module with a new binner is possible
	Bin_refinement
		major speed improvement with new --quick option, especially on low-memory systems
		major big fix that caused the module to sometimes needlessly throw away good bins, especially at lower completion thresholds (-c)
		advanced cleanup if using an existing output directory
		improved error and status messages
		fixed bug that created dandom tmp files in output directory when using two bin sets
		output metawrap folder is now in lower case
	Blobology
		added failsafe if assembly file does not exist
	Kraken
		added help message details
		added progress messages during kraken translation process
	Quant_bins
		added exception that skips making the heatmap when the sample count is only 1
		fixed error causing the heatmap funciton to fail due to bool error
		added failsafes to make sure that the bin and total assembly contig naming is the same


metaWRAP v=1.0 (September 2018)
	General
		removed gcc dependancy to prevent library errors with concoct
		cleaned up some help messages
		added --show-config option to metawrap to display program configuration details
		improved installation documentation
	Assembly
		changed option name --use-metaspades to --metaspades
		changed option name --use-megahit to --megahit
		default memory allowance is now 24GB
	Quant_bins
		the -a option is now optional, but strongly recommended
		the bin abundance heatmap is now standardized to the total abundance of the bins, not the reads
	Reassemble_bins
		added -l option to specify minimum contig length
		default memory allowance is now 40GB
	Classify_bins
		fixed major bug that resulted inacurate classification due to mis-calculating contig lengths
		Fixed major bug that caused the module to ignore the last contig in each bin
		fixed bug that caused crashes when a contig was classified as "subfamily"
	Bin_refinement
		default memory allowance is now 40GB

metaWRAP v=0.9 (June 2018)
	General
		fixed major bug with running metawrap in a custom conda environments
		fixed bug caused by multiple metawrap installations
		bin/metaWRAP excecutable is not a symlink pointing to bin/metawrap
	Bin_refinement
		fixed bug with plotting refinement iterations
		delete bins that have a size 0 after dereplication
		fixed shebang in summarize_checkm.py
		allowed pplacer to use multiple threads, drastically speeding up the module
		module no longer clears output DIR before starting. safer this way
	Binning
		nos uspports single-end read inputs
		added metabat1 binning option
		fixed checkm tmp directory handling when using the --run-checkm option
		fixed perl5 library handling when running maxbin2
		added diagnostic info for perl libraries
		added use of MaxBin v2.2.5 - this fixes some issues with newer gcc
		checkm now uses pplacer multi-threading
	Blobology
		added figure output folders for easier viewing
	Kraken
		removed -a option from ktImportText
		added checkpoint to make sure that fasta or fastq inputs are given
	Annotate_bins
		fixed perl5 library handling when running prokka
		added minced dependancy
		added diagnostic info for perl libraries
	Classify_bins
		removed percent confidance values for each classification
	Assembly
		use metaSPAdes v3.12.0
	Reassemble_bins
		read alignemnt and splitting is now  done simultaneously, and no longer requires a lot of RAM
		signifficantly sped up the read-splitting function and prevented freezes
		added and fixed --parallel option bug
		use SPAdes v3.12.0
		checkm now uses multi-threading for pplacer
		the user can now change the strict/permissive read mapping SNP cut off parameters


metaWRAP v=0.8 (March 2018)
	General
		every module now returns the total run time at the end
		every module now gives the full run command back
		added trim-galore dependancy to conda installation
	Conda installation:
		added R dependancy
		fixed channel ordering
		metaWRAP now immediately exits if it cannot find the config file
	Read_qc:
		removed unnecessary large intermediate files
		added clean-up feature
		--skip-bmtagger flag now properly works
	Binning:
		fixed bug that caused maxbin to fail with absolute path
		removed unnecessary large intermediate files
		added pre- and post-run clean-up feature
		removed CPU bottleneck from the read alignment stage
	Bin_refinement
		added output dir cleanup at start of module if the directory already exists
		added extra debugging info during run
		.stats files now contain the proper binner source in the last column
		fixed bug caused by "=" characters in contig naming
	Reassemble_bins:
		changed  plotting color scheme
		removed last column (useless NA values)
	Blobology
		added clean-up feature
		plotting bugfixes
		added more colors for bin labeling
		fixed axis labels
		fixed bug with error handling when bin and assembly contig sdont match
	Quant_bins
		fixed bug that threw an error when contig names had spaces
		fixed bug that would caused the last contig in the assembly file to not be read
	Annotate_bins
		fixed improper perl5 library handling on some systems
		removed parallelization of prokka (did not work on all systems)
		improved error handling
	Kraken
		added -a option to ktImportText - now kronas do not require internet to view
		changed krona tools version requirement to 2.5 to allow for -a option


metaWRAP v=0.7 (January 2017)
	Conda installation:
		removed gcc as a run dependancy to help resolve gcc library issues on some servers
		changed taxator-tk version from 1.3.3 to 1.3.3e, which sources from a more updated binary source
	Quant_bins module:
		fixed bug where quantitation would fail if the contig names had a different naming conventaion from metaSPAdes
		improved run time by not making unnecesary coppies of assembly	
	Classify_bins module:
		fixed bug in processing columns of the blast output
	Bin_refinement:
		improved error handling
		fixed bugs related to plot making
	New module: Annotate_bins:
		quickly functionally annotate a set of bins with PROKKA


metaWRAP v=0.6 (Late December 2017)
	General:
		completely moved to installation of metaWRAP and ALL dependancies with conda
		added detailed database download and configuration instructions
		reduced benign mkdir errors throughout
	Assembly module:
		fixed tmp directory handeling bug
	Kraken module:
		fixed major bug preventing subsetting reads if there were spaces in the read identifiers
		added jellyfish v=1.1.11 to conda env file for kraken-build
	Reassembly module:
		major bug fixes with tmp directory handling
		restored parallelization of SPAdes - all bins assemble simmultaneously with 1 thread now
	

metaWRAP v=0.5 (Mid December 2017)
	General:
		Added overview flowcharts for most modules, and updated older flowcharts
		metaWRAP is now much more binning oriented (see overview flowchart)
	Assembly module:
		added minimum contig length option (defore the default was 1000bp)
		sped up megahit assembly re-formatting by removing redundant sorting operations
	Bin_refinement module:
		parallelized Binning_refiner such that all four hydridizing operations sun simultaneously
	Reassemble_bins module:
		added plotting functiong to summarize the N50, completion, and contamination rankings of the before and after bins
	New module: Classify bins:
		Uses MEGABLAST to align the contigs in bins to RefSeq
		Taxator-tx asigns taxonomy to each contig
		Use weighted tree algorythm to find consensus taxonomy of each bin


metaWRAP v=0.4 (Early December 2017)
	General:
		Most dependancies can now be installed with a pre-configured conda environment
	Binning module:
		Added option to immediately run CheckM on resulting bins
	ReadQC module:
		Major bug fix that prevented bmtagger from filtering out human reads when the read names in the fastq had spaces
		Module now exits if the provided fastq files do not exist
	Bin_refinement: this module consolidats all possible binning version of the bins from the Binning module
		added contig dereplication to avoid situations where a contig ends up in more than one bin
		removed depricated requirement for prviding reads as input
		major bug fit to prevent HMMER to run out of space in /tmp/ by providing a new tmp folder
		bug fix: bin consolidation script now supports contigs in any naming format
		added plotting functiong to summarize the completion and contamination rankings of the inputs, intermediate interations, and final output
	Bin_reassembly: this modules takes a set of metagenomic reads, alignes them back to the bins, and uses those reads to reassemble them
		removed spades parallelization due to strange signmentation fault errors...
		majob bug fix of bug preventing recruiting of reads for reassembly if the read names had spaces in them
		major bug fit to prevent HMMER to run out of space in /tmp/ by providing a new tmp folder


metaWRAP v=0.3 (November 2017)
	General:
		Error handling is greatly improved throughout the pipelines by incorporating the $? error code instead of relying on output files
		Disabled PHYLOSIFT module (this software is too old)
		Temporarily disabled ALL module due to increased complexity of the metaWRAP pipeline
	ReadQC module:
		Fixed issue with program thinking READQC did not finish correctly
	Assembly module:
		Removed joint assembly feature. Now you can only assemble with metaSPAdes OR Megahit.
		(megahit is defualt due to its speed)
		Changed minimum contig length from 500bp to 1000bp
	Binning module:
		This module is now split into four parts for modularity:
		Binning module: this module is a basic wrapper around existing binning software (but conviniently handles intermediate files)
			You can now bin with metaBAT2 and/or MaxBin2 and/or CONCOCT
			Pipeline now calculates library insert sizes on the fly (and correctly)
			Samtools tmp files bug fix
			Samtools sort -m memory option fixes
		Bin_refinement: this module consolidats all possible binning version of the bins from the Binning module
			Runs CheckM on binning iterations
			Produces the best possible bins
			Allows user to input the minimum desired completion and maximum contamination
			No longer quits if there are too many bins to plot
		Bin_reassembly: this modules takes a set of metagenomic reads, alignes them back to the bins, and uses those reads to reassemble them
			The reassembly function as a whole is now 100+ times faster than before due to paralelization
			The read filtering for each bin is now parallelized into the same BWA alignment operation
			The reassembly itself is not parallelized into 1 thread operations for each bin, which ends up being much faster
		Quant_bins:
			This module takes in (non-reassembled) bins and reads from many samples, and estimates the abundance of each bin in each sample with salmon
			The process is paralelized and the alignment time does not scale with number of bins
	Blobology module:
		Allows for paralel processing of multiple read sets (but one assembly). Produces one figure per sample, with colors being consistant.
		Changed annotations to blobplot file when the --bins option is selected - added additional columns
		Now makes multiple bin annotation plots, annotating bins and their taxonomy
		Blastn does not re-run if there is an output file with the same name already in the output folder


metaWRAP v=0.2 (August 2017)
	General:
		Added compatibility with long input parameters (eg. --options asdf) with getopt instead of getopts
		Chenged instalation style of metaWRAP so that the contents of bin needs to be added to PATH to run. The user still needs to edit the config file first
		Changed name of contig.sh to config-metawrap so be more distinguishable in PATH
		All modules are now called through the master "metaWRAP" script (including the ALL module)
		Changed heirarchy of pipeline scripts. Now they are hidden away in a "pipelines" folder, and only metaWRAP is visible
		Changed the commenting system to be done through a python script that writes out pretty comments
		New module: Phylosift. Currently all it does is randomly subsamples reads and runs Phylosift on them	
	ReadQC module:
		Added --skip-bmtagger option (reduces runtime signifficantly)
		Added --skip-trimming option
		Added --skip-pre-qc-report option
		Added --skip-post-qc-report option
	Assembly module:
		Added --only-metaspades option (for those who dont like the idea of double assembly)
		Added --only-megahit option (signifficantly reduces resourse requirements and time)
	Binning module:
		Added --skip-checkm option (reduces runtime)
		New feature where bins that are >20% completion and <10% contamination are placed into a new folder - "good bins"
		Added --checkm-good-bins option, to allow making a checkm figure for only good bins (makes a prettier figure)
		Added --skip-reassembly option (reduces runtime signifficantly)
		New feature where after reassembly the best variant of each bin (original, strict, or permissive reassemblies) is placed into a new folder - "best bins"
		Added --checkm-best-bins option, to allow re-making the checkm figure on only the best versions of each bin
		Removed KRAKEN from the binning module. KRAKEN now has to be run seperately on the output bins
		Not also returns the average and stdev of insert lengths for each sample - useful for library assessment
	Blobology module:
		Added --bins option, which allows to annotate the blobplot with bins from a binning folder
	ALL module:
		Major bug fixes and improvements
		Added a Phylosift and Kraken on bins steps to pipeline
		All output figures and reports are now saved to "metaWRAP_figures" folder at the end of the pipeline
		Added --fast option, which skips some non-essential and computationally expensive parts of the pipeline


metaWRAP v=0.1 (July 2017)
	First user-friendly version of metaWRAP!