detaxizer - detaxizer 1.2.0 - Kunschd

Summary of changes

• filtering is set now by default
• defaults reflect best settings from benchmarking human decontamination
• improvements to memory and time requirements

Detailed changes

Added

• PR #70 - Filtering is now default, --skip_filter was added (by @d4straub)
• PR #71 - Add usage information learned from our benchmarking (by @d4straub)

Changed

• PR #65,PR #69 - Template update for nf-core/tools 3.3.2 (by @d4straub)
• PR #72 - Default for --kraken2db was changed from 'https://genome-idx.s3.amazonaws.com/kraken/k2standard08gb20240904.tar.gz' to 'https://genome-idx.s3.amazonaws.com/kraken/k2standard_20240605.tar.gz'. That database is much larger (60GB) but default settings will therefore reflect best decontamination performance in benchmarks (by @d4straub)
• PR #73 - Doubled memory allocation for ISOLATEBBDUKIDS (by @d4straub)
• PR #75 - Updated version and contributors (by @d4straub)

Fixed

• PR #62 - Use dnaio to reduce memory spikes during renaming (by @bede)
• PR #77 - Fixed conda versions to exactly follow container versions (by @d4straub)
• PR #78 - Update typos, re-add code comments (by @d4straub)

Dependencies

| Software | Previous version | New version | | -------- | ---------------- | ----------- | | MultiQC | 1.27 | 1.29 | | tar | 1.3 | 1.34 |

Removed

• PR #70 - Filtering is now default, --enable_filter was removed and replaced by --skip_filter (by @d4straub)

- Nextflow
Published by d4straub 7 months ago

detaxizer - 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/k2standard08gb20231009.tar.gz' | 'https://genome-idx.s3.amazonaws.com/kraken/k2standard08gb20240605.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 fastabbduk; necessary to further distinguish the two parameters | | `--skipblastn|--validationblastn| blastn is now to be enabled on purpose; too resource intensive for a default setting | |--maxcpus| - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits),resourceLimitscan now be set via a config | |--maxmemory| - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits),resourceLimitscan now be set via a config | |--maxtime| - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits),resourceLimits` can now be set via a config |

- Nextflow
Published by jannikseidelQBiC over 1 year ago

detaxizer - 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)

- Nextflow
Published by jannikseidelQBiC almost 2 years ago