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CHANGELOG.md

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Version 0.5.1

Outputs:

  • Illumina dehosted fastq files are now generated from the dehosted bam files sorted with the samtools sort -n flag
    • Previously it was just samtools sort <BAM>
    • Should address inconsistent instances of illumina reads not being output in proper pairs

General Developer Changes:

  • Samtools sort added as its own module following either composite mapping or amplicon downsampling
    • Amplicon downsampling now has a sort command before it but not after
      • Illumina and Nanopore pipelines updated appropriately for this
  • Added new test for mapping illumina after it is output from the pipeline
    • Mostly to see if bwa mem is having issues mapping the final files
  • Fixed some spacing/formatting in
    • Illumina workflow
    • Illumina modules
    • Nanopore modules

Version 0.5.0

General Developer Changes:

  • Adjusted all labels and resources to be in line with nf-core
    • Added timeouts to processes as well

Version 0.4.0

Additions:

  • Added downsampling and its params
    • Adds seqtk as a dependency to the environments
    • Random downsampling with seqtk option
    • Amplicon downsampling with samtools option
  • Additional columns in the removal summary file if downsampling is used
    • downsample_maximum_reads
    • downsample_seed
  • Mamba profile added
    • Conda profile no longer defaults to using mamba

Environment Adjustments:

  • Specified versions for the following tools in the nanopore and illumina environment files:
    • samtools=1.17
    • python=3.10
    • pysam=0.21.0
    • seqtk=1.4
    • minimap2=2.26

General Developer Changes:

  • Changed logic on how --flat is works with nanopore dehosting
    • No longer a different process module
  • Updated some of the outputs to be path rather than file
  • Adjusted how the versions output is created
  • Adjusted formatting of modules to make them easier to read

Version 0.3.0

General Developer Changes:

  • Changed how conda is implemented to match nextflow version updates
  • Fixed tests

Version 0.2.0

Argument Changes:

  • Added --keep_ref_id <ID> as an argument for illumina and nanopore fastq data
    • Allows for a different reference ID to be kept if the reference sequence is changed
  • Removed --covid_ref_id <ID> as an illumina specific argument
    • Replaced by above
  • Removed the illumina_threads and nanopore_threads resource arguments that were not super useful
    • Changed to using task.cpus to keep everything in line
    • Resources should be changed using the process name or the process tag now

Parameter Changes:

  • Default minimum read length for nanopore data (--min_length) set to 350 from 400 to better accommodate shorter amplicon schemes
  • Help command updated

Output Changes:

  • New output file: process_versions.yml
    • File contains process name along with tools and their versions used in it

General Developer Changes:

  • Changed code order for nanopore workflows
    • All minimap2 code should be above nanostripper in the files now
  • General reformatting of code to try to make everything more consistent/cohesive
  • Moved the minimap2 workflow above the nanostripper workflow in all processes

Version 0.1.0

Argument Changes:

  • Nanopore Nanostripper Pipeline:
    • Accessed with --nanopore and --nanostripper flags
    • Fast5 input changed from --directory to --fast5_directory

Added Functionalities:

  • Added nanopore fastq host removal pipeline focused on minimap2
    • dehost_nanopore.py to accompany this
  • Added help statement module that is printed when --help is passed
  • Added pysam and pip to nanopore environment

General Developer Changes:

  • DSL2 enabled (no longer on DSL2 preview)
    • Small changes to some modules to address this but no functionality changes
    • Nextflow version >= 21.04.0 needed
  • Adjusted labels for CPU and MEM usage
    • mediumMem replaces mediumCPU
  • Adjusted config file structure
  • Adjusted how modules are imported
  • Adjusted some nanopore module names to not overlap
    • nanoporeDehosting -> nanoporeNanostripperDehosting
    • fastqSizeSelection -> fastqSizeSelection_NS
    • regenerateFast5s -> regenerateFast5s_NS

Version 0.0.1

  • Initial Release that works