2.0.0 - Saffron Vulture

2.0.0 - 'Saffron Vulture' - [2026-09-18]

This is a major release, with breaking changes.

The pipeline now implements topics to collect software version, the minimum nextflow version is 25.10.4.

v2.0.0 of genomeassembler is a large refactor of the pipeline to facilitate sample-level parameteristation. This allows to either parameterise the pipeline using params, or parameterise samples via the input samplesheet. In case both types of parameterisations are used, sample parameters will take priority.

Since this workflow follows a sample-centric implementation, nextflow will always render the full pipeline dag, but depending on configuration samples may not travel through the whole pipeline. This may also cause terminal output to show task instances that will never become an active process.

In addition, v2.0.0 contains these changes:

Added

Pull requests in reverse chronological order since v1.1.0

#215

• Prepare samplesheet for downstream QC with nf-core/genomeqc

#212

• bumped medaka to 2.2.2

#207

• additional tests for QC modules

• Report can now deal with QUAST runs without reference

#203

• Switched to nf-schema for input parsing

• Added test with HiC dataset (kindly prepared by @OlivierCoen).

#198

• Simplifies changes to ensure bgzipped outputs introduced in #192.

#197

• Fix handling of reads for quality control, inputs for jellyfish should be trimmed.

#196

• bgzip medaka outputs

#195

• Fixed oversight in #171 where hifi reads were not assembled via flye with strategy single.

#194

• Update CONTRIBUTING.md.

#193

• Update OUTPUT.md with bgzipped files.

#192

• BGZIP is now used for all fasta outputs, input for SAMTOOLS_FAIDX is no longer unzipped.

#171

• fastplong for long-read trimming and qc
• fastp for short-read trimming and qc
• migration to nf-test
• increased flexibility of the scaffolding strategy
• added option to group samples
• dorado polish added as an alternative to medaka for ONT polishing. This is an experimental feature, due to dorado being under active development.
• HiC scaffolding subworkflow:
  • mapping with bwamem2 or minimap2
  • duplicate removal with picard
  • scaffolding with yahs
• Switched to the versions topic, requires nextflow >=25.10.4

#185

• Template update to 4.0.2

#180

• Template update to 3.5.1

#177

• Template update to 3.4.1

#164

• Template update to 3.3.1

Fixed

#176

• Fixed typo in medaka url (@TomHarrop)

#223

• Add exitcode 2 as retry code for links in AWS fulltest profile.

#230

• Increase estimated memory for bwa-mem2 since inputs are bgzipped.

Dependencies

New

The following modules have been added:

name	v1.1.0	v2.0.0
dorado	-	1.3.1+7c84b01de
bwamem2	-	2.3
fastp	-	1.3.6
fastplong	-	0.4.1
gfatools	-	0.5
htslib	-	1.24.
picard	-	3.5.0
yahs	-	1.2.2

Updated

The following tools have been updated to a new version:

name	v1.1.0	v2.0.0
busco	5.8.3	6.1.0
genomescope2	2.0	2.0.0
medaka	2.0.1	2.2.2
minimap2	2.29	2.30

Deprecated

The following tools have been deprecated:

name	v1.1.0	v2.0.0
nanoq	0.10.0	deprecated
lima	2.12.0	deprecated
porechop	0.2.4	deprecated
pigz	2.8	deprecated with porechop
trimgalore	0.6.10	deprecated
cutadapt	4.9	deprecated

The following param is no longer implemented:

• dump, used to dump jellyfish output.

Unchanged

The following tools are unchanged:

name	v1.1.0	v2.0.0
coreutils	9.5	9.5
jellyfish	2.3.1	2.3.1
longstitch	1.0.5	1.0.5
quast	5.3.0	5.3.0
quarto	1.7.31	1.7.31
fastqc	0.12.1	0.12.1
flye	2.9.5	2.9.5
hifiasm	0.25.0	0.25.0
liftoff	1.6.3	1.6.3
links	2.0.1	2.0.1
merqury	1.3	1.3
meryl	1.4.1	1.4.1
samtools	1.21	1.21
pilon	1.24	1.24
ragtag	2.1.0	2.1.0