Nextflow Registry | nf-core/merfin/hist@0.0.0-0c7146d

nf-core/merfin/hist @ 0.0.0-0c7146d

Compare k-mer frequency in reads and assembly to devise the metrics K* and QV*

assembly evaluation quality completeness

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @rodtheo

Maintainers: @rodtheo

Compare k-mer frequency in reads and assembly to devise the metrics K* and QV*

Add the following snippet to your workflow script to include this module.

include { MERFIN_HIST } from 'nf-core/merfin/hist'

MIT License

Process

`Name`	`MERFIN_HIST`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta_assembly` file	Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED] `*.{fasta, fasta.gz}`

#2 tuple

`meta1` map	Groovy Map containing sample read information e.g. `[ id:'sample1', single_end:false ]`
`meryl_db_reads` file	K-mer database produced from raw reads using Meryl [REQUIRED] `*.{meryl_db}`

`lookup_table` file	Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL] `lookup_table.txt`

`seqmers` file	Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL] `*.{meryl_db}`

`peak` float	Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED]

Output 3 channels

#1 hist tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.hist` file	The generated 0-centered k* histogram for sequences in <fasta_assembly.fasta>. Positive k* values are expected collapsed copies. Negative k* values are expected expanded copies. Closer to 0 means the expected and found k-mers are well balanced, 1:1. `*.{hist}`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 log_stderr tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.hist.stderr.log` file	Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end. `*.{hist.stderr.log}`

Tool	Description	Homepage
merfin	Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.	https://github.com/arangrhie/merfin

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:54:43 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmerfin%2Fhist/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/merfin/hist/blobs/sha256:6afc42542836a39e441ffb18440a398514a8db64ffc3547c60f7c7f56d0b2915
Size	4.4 KB
Checksum	sha256:6afc42542836a39e441ffb18440a398514a8db64ffc3547c60f7c7f56d0b2915
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:54:43 (UTC)		1	4.4 KB	-