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nf-core/nanoseq v3.0.0 - Zinc Kea
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@yuukiiwa yuukiiwa released this 20 Jun 10:44
· 73 commits to master since this release
3.0.0
1e60482
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Learn about vigilant mode.

Major enhancements

  • Add DNA variant calling functionality
  • Add RNA modification and fusion detection functionalities
  • Add demux_fast5 module to output demultiplexed fast5 files when --output_demultiplex_fast5 is set
  • Add --trim_barcodes in Guppy basecaller to trim the barcodes from output fastq
  • Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
  • Removed --publish_dir_mode as it is no longer required for the new syntax
  • Bump minimum Nextflow version from 21.04.0 -> 21.10.3
  • Update pipeline template to nf-core/tools 2.2
  • Update bambu version from 1.0.2 to 2.0.0
  • Update multiqc version from 1.10.1 to 1.11

Parameters

  • Added --output_demultiplex_fast5 to output demultiplexed fast5
  • Added --trim_barcodes in Guppy basecaller to trim the barcodes from output fastq
  • Added --call_variants to detect DNA variants
  • Added --split_mnps to split multi-nucleotide polymorphisms into single nucleotide polymorphisms when using medaka
  • Added --phase_vcf to output a phased vcf when using medaka
  • Added --deepvariant_gpu to use gpu with docker pepper_margin_deepvariant
  • Added --skip_vc to skip variant_calling
  • Added --skip_sv to skip structural_variant_calling
  • Added --variant_caller to specify variant caller.
  • Added --structural_variant_caller to specify structural variant caller
  • Added --skip_modification_analysis to skip RNA modification detection
  • Added --skip_xpore to skip xpore
  • Added --skip_m6anet to skip m6anet
  • Added --skip_fusion_analysis to skip RNA fusion detection
  • Added --jaffal_ref_dir to indicate the reference directory path required by JAFFAL

Software dependencies

Dependency Old version New version
bioconductor-bambu 1.0.2 2.0.0
bioconductor-bsgenome 1.58.0 1.62.0
cutesv 1.0.12
deepvariant 1.0.3
jaffa 2.0
m6anet 1.0
medaka 1.4.4
multiqc 1.10.1 1.11
ont_fast5_api 4.0.0
pepper_margin_deepvariant 0.8
pepper_margin_deepvariant_gpu 0.8
samtools 1.14 1.15
sniffles 1.0.12
xpore 2.1

Bug fix

  • The GET_TEST_DATA process now uses checks for any file in the path.
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