v0.12

• Fix bug with method invocation error on _closure
• Incorporate required code to run on cloudgene

v0.11

• Set rows with no hits to have a null value across all columns of the html report
• Automatically check for adapter in pipeline (ie remove adapter_trimming parameter)
• Catch polishing step error
• Add a "Flag definitions" button at the bottom of the report
• Derive a partial report for cases where clustering or blast search fail
• Create legend for interpretation of the BAM linked to html report
• Set quality filtering to TRUE and mean quality to 8 by default
• Fix grey colour display in html report
• Update workflow image so it shows location of outputs in the results output folders

v0.10

• Change target organism delimiter from semi-colon to pipe to match pipeline 2
• Update raw_reads_flag and qfilter_flag thresholds in qc report based on latest feedback from DAFF.
• Add a flags.csv file which describes each flag and provides thresholds on which the colouring system is based.
• Remove the target organism flag from the confidence score.
• Incorporate section about flags and confidence score in the READ.ME file.
• Prevent pipeline from stalling if blast or clustering step fails for a sample.
• Generate a status.txt file which provides completion status of rattle and blast processes. Feed these to the HTML report.
• Provide base quality for the final consensus matches as fastq.
• Update name of BAM file mapping back to reference to _ref_aln.sorted.bam.bam.
• Specify in the README documentation that special characters are not permitted in sample names.
• Add details of samtools consensus configuration in README documentation.
• Add sentence about how to modify log name and path in README documentation.

v0.9

• report the % of reads whose length match 90% instead of 80% of the reference for the READ_LENGTH_FLAG
• incorporate a confidence score that takes into account all the current flags. Currently all flags are given the same weight
• colour the consensus in the html report based on normalised confidence score (which ranges from 0-1)
• fix bug which requested for path to MetaCOXI database to be provided even if gene targetted was not COI
• gene name for cytochrome oxydase I can be specified as CO1 and COI in target_gene
• break external links for the save as read-only feature of the html report

v0.8

• Fix bam file link in HTML report
• Incorporate a % read length flag
• Implement a Save button option to break external file links
• Display correct % of consensus sequences matching a BLAST reference sequence

v0.7

• Specify samplename at start of HTML report and associated bam file.
• Provide a python script to help with the creation of a samplesheet. It can handle a folder with subfolders of multiple fastq.gz files per sample or a folder with single fastq.gz files per sample.
• Enable the search of multiple target organisms per sample.
• Improve term search so it matches exactly a species name.
• Enable subsampling (by default, subsampling is set to 10,000 reads).
• Add fields in the samplesheet file to accommodate test and method from LIMS.
• Force specification of COI database if COI gene specified.
• Return an error if any rows for the required fields in the samplesheet have an empty value
• Return an error if any row for target_size is not an integer.

v0.6

Pipeline halts the analysis for the the samples for which the clustering failed but keeps on with the analysis for the other samples

v0.5

• Fig bug so Viruses category is displayed in Broad category classification
• Display User name and Facility in html report
• Display default parameters and user defined parameters in html report
• Display tools version
• Update the versions.yml file to the correct format
• Enable to save first name and last name for analyst
• Enable to screen for species in the target_organism

v0.4

• Update installation section regarding metacoxI and WSL for windows machines in the README file.
• Incorporate the log from RATTLE.

v0.3

• Update code to deal with NCBI taxonomic category update in taxdump files.
• Prevent the pipeline from running if fastq.gz files provided were derived using fast basecalling model.
• Update the README file to include a section about how to set the singularity cache directory.
• Describe the --publishdir parameter in the README file.
• Remove superfluous files in the results folder.
• Order results folder in numerical order.
• Fix bug identified for the map to reference process.
• Update index header column names.