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nf-core/nanoseq: Changelog

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

[3.0.0] - 2022-06-21

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.

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

[2.0.1] - 2021-11-29

Bug fix

  • The UCSC_BEDGRAPHTOBIGWIG process now uses the ucsc-bedgraphtobigwig container
  • The full-size and minimal AWS tests have successfully finished after changing to the ucsc-bedgraphtobigwig container

[2.0.0] - 2021-11-26

Major enhancements

  • Pipeline has been re-implemented in Nextflow DSL2
  • Software containers are now obtained from Biocontainers
  • Update pipeline template to nf-core/tools 2.1
  • #77 - Skipped alignment steps
  • #97 - Add optional DNA cleaning option

Parameters

  • Added --run_nanolyse to run NanoLyse for DNA cleaning of FastQ files
  • Added --nanolyse_fasta to provide a fasta file for nanolyse to filter against

Software dependencies

Dependency Old version New version
bioconductor-bambu 1.0.0 1.0.2
nanolyse 1.2.0
r-base 4.0.3 4.0.2

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

[1.1.0] - 2020-11-06

Major enhancements

  • Transcript reconstruction and quantification (bambu or StringTie2 and featureCounts)
  • Differential expression analysis at the gene-level (DESeq2) and transcript-level (DEXSeq)
  • Ability to provide BAM input to the pipeline
  • Change samplesheet format to be more flexible to BAM input files
  • Add pycoQC and featureCounts output to MultiQC report
  • Add AWS full-sized test data
  • Add parameter JSON schema for pipeline
  • Add citations file
  • Update pipeline template to nf-core/tools 1.11
  • Collapsible sections for output files in docs/output.md
  • Replace set with tuple and file with path in input section of all processes
  • Capitalise process names
  • Added --gpus all to Docker runOptions when using GPU as mentioned here
  • Cannot invoke method containsKey() on null object when --igenomes_ignore is set #76

Parameters

  • Added --barcode_both_ends requires barcode on both ends for Guppy basecaller
  • Added --quantification_method to specify the transcript quantification method to use
  • Added --skip_quantification to skip transcript quantification and differential analysis
  • Added --skip_differential_analysis to skip differential analysis with DESeq2 and DEXSeq
  • Added --publish_dir_mode to customise method of publishing results to output directory nf-core/tools#585

Software dependencies

Dependency Old version New version
Guppy 3.4.4 4.0.14
markdown 3.1.1 3.3.3
multiqc 1.8 1.9
nanoplot 1.28.4 1.32.1
pygments 2.5.2 2.7.2
pymdown-extensions 6.0 8.0.1
python 3.7.3 3.8.6
samtools 1.9 1.11
ucsc-bedgraphtobigwig 357 377
ucsc-bedtobigbed 357 377
bioconductor-bambu - 1.0.0
bioconductor-bsgenome - 1.58.0
bioconductor-deseq2 - 1.30.0
bioconductor-dexseq - 1.36.0
bioconductor-drimseq - 1.18.0
bioconductor-stager - 1.12.0
r-base - 4.0.3
seaborn - 0.10.1
stringtie - 2.1.4
subread - 2.0.1
psutil - -

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

[1.0.0] - 2020-03-05

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