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CHANGELOG.md

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nf-core/detaxizer: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.1.0 - Kombjuudr - [2024-11-08]

Added

  • PR #34 - Added bbduk to the classification step (kraken2 as default, both can be run together) (by @jannikseidelQBiC)
  • PR #34 - Added --fasta_bbduk parameter to provide a fasta file with contaminants (by @jannikseidelQBiC)
  • PR #34 - Rewrote summary step of classification to be usable with bbduk and/or kraken2 (by @jannikseidelQBiC)
  • PR #34 - Made preprocessing with fastp optional and added the parameter --fastp_eval_duplication to turn on duplication removal (off as default, was on/not changeable in v1.0.0) (by @jannikseidelQBiC)
  • PR #34 - Optionally the removed reads can now be written to the output folder (by @jannikseidelQBiC)
  • PR #34 - Added optional classification of filtered and removed reads via kraken2 (by @jannikseidelQBiC)
  • PR #39 - Added generation of input samplesheet for nf-core/mag, nf-core/taxprofiler (by @Joon-Klaps)

Parameters

Added parameters:

Parameter
--fasta_bbduk
--preprocessing
--output_removed_reads
--classification_kraken2
--classification_bbduk
--kraken2confidence_filtered
--kraken2confidence_removed
--classification_kraken2_post_filtering
--fastp_eval_duplication
--bbduk_kmers

Changed default values of parameters:

Parameter Old default value New default value
--fastp_cut_mean_quality 15 1
--kraken2db 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz' 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20240605.tar.gz'
--kraken2confidence 0.05 0.00
--tax2filter 'Homo' 'Homo sapiens'
--cutoff_tax2filter 2 0
--cutoff_tax2keep 0.5 0.0

Changed

Fixed

  • PR #33 - Addition of quotation marks in parse_kraken2report.nf prevents failure of the pipeline when using a taxon with space (e.g. Homo sapiens) with the --tax2filter parameter (by @jannikseidelQBiC)
  • PR #34 - Made validation via blastn optional by default (by @jannikseidelQBiC)
  • PR #34 - Changed parameter --fasta to --fasta_blastn (by @jannikseidelQBiC)

Dependencies

Updated and added dependencies

Tool Previous version Current version
bbmap - 39.10
blastn 2.14.1 2.15.0
multiQC 1.21 1.25.1
kraken2 2.1.2 2.1.3
seqkit 2.8.0 2.8.2

Deprecated

Parameter New parameter Reason
--fasta --fasta_blastn Introduction of fasta_bbduk; necessary to further distinguish the two parameters
--skip_blastn --validation_blastn blastn is now to be enabled on purpose; too resource intensive for a default setting
--max_cpus - New behavior of nextflow, resourceLimits can now be set via a config
--max_memory - New behavior of nextflow, resourceLimits can now be set via a config
--max_time - New behavior of nextflow, resourceLimits can now be set via a config

v1.0.0 - Kobbfarbad - [2024-03-26]

Initial release of nf-core/detaxizer, created with the nf-core template.

Added

  • Added preprocessing part of workflow (tool: fastp)
  • Added examination part of workflow (tools: kraken2 and optionally blastn) and a summary step for this part
  • Added optional filtering step (either applied to raw reads or preprocessed ones, and either with the output of kraken2 or blastn)
  • Added read renaming step at the beginning and end of the workflow to cope with different fastq header formats while keeping original headers in the filtered fastqs

Fixed

Dependencies

Deprecated