nf-core/nanoseq v3.1.0 - NObelium Guppy

Major enhancements

• Removed the guppy basecaller as distributing it via a docker image is a breach to EULA
• Bump minimum Nextflow version from 21.10.3 -> 21.10.3
• Update pipeline template to nf-core/tools 2.7.2
• Update bambu version from 1.0.2 to 2.0.0

Parameters

• Removed --flowcell as nanoseq no longer supports basecalling
• Removed --kit as nanoseq no longer supports basecalling
• Removed --guppy_config as nanoseq no longer supports basecalling
• Removed --guppy_model as nanoseq no longer supports basecalling
• Removed --guppy_gpu as nanoseq no longer supports basecalling
• Removed --guppy_gpu_runners as nanoseq no longer supports basecalling
• Removed --guppy_cpu_threads as nanoseq no longer supports basecalling
• Removed --output_demultiplex_fast5 as nanoseq no longer supports basecalling
• Removed --skip_basecalling as nanoseq no longer supports basecalling
• Removed --skip_pycoqc as nanoseq no longer supports basecalling

Software dependencies

Dependency	Old version	New version
bioconductor-bambu	2.0.0	3.0.8

nf-core/nanoseq v3.0.0 - Zinc Kea

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.

nf-core/nanoseq v2.0.1 - Steel Sloth

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

nf-core/nanoseq v2.0.0 - Nickel Sloth

[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.

nf-core/nanoseq v1.1.0 - Green Panda

[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.

nf-core/nanoseq v1.0.0 - Silver Snail

[1.0.0] - 2020-03-05

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