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