detaxizer 1.1.0 - Kombjuudr

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

• PR #42 - Template update for nf-core/tools 3.0.2, for details read this blog post

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

detaxizer 1.0.0 Kobbfarbad

First release of nf-core/detaxizer!

This is the initial version of the pipeline:

1. Read QC (FastQC)
2. Pre-processing (fastp)
3. Classification of reads (Kraken2)
4. Optional validation of searched taxon/taxa (blastn)
5. Optional filtering of the searched taxon/taxa from the reads (either from the raw files or the preprocessed reads, using either the output from kraken2 or blastn)
6. Summary of the processes (how many reads were initially present after preprocessing, how many were classified as the tax2filter plus potential taxonomic subtree and optionally how many were validated)
7. Present QC for raw reads (MultiQC)