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nf-core/crabs/import @ 0.0.0-6c4ed3a

In-house generated or curated data can be imported into CRABS.

insilico amplicon sequencing inhouse
Latest version: 0.0.0-6c4ed3a
Total downloads: 8
Source: nf-core/modules
Authors: @famosab @a4000
Maintainers: @famosab @a4000

Summary

In-house generated or curated data can be imported into CRABS.

Get started

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

include { CRABS_IMPORT } from 'nf-core/crabs/import'

License

MIT License

Process
Name CRABS_IMPORT
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
fasta file

In-house sequencing data

 *.{fa,fasta}
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'sample1' ]
accession2taxid file

Linking accession numbers to taxonomic IDs

 *.accession2taxid
#3 tuple
meta3 map

Groovy Map containing sample information e.g. [ id:'sample1' ]
names file

Containing information about the phylogenetic name associated with each taxonomic ID

 *.dmp
#4 tuple
meta4 map

Groovy Map containing sample information e.g. [ id:'sample1' ]
nodes file

Containing information how taxonomic IDs are linked

 *.dmp
import_format string

Name of the repository from which the data was downloaded, i.e., BOLD, EMBL, GreenGenes, MIDORI, MITOFISH, NCBI, SILVA, or UNITE.
Output 2 channels
#1 crabsdb tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.txt file

Reverse complemented Sequence

 *.txt
#2 versions_crabs tuple
${task.process} string

The name of the process
crabs string

The name of the tool
crabs --help 2>/dev/null | grep -oE 'v[0-9.]+' | cut -c2- eval

The expression to obtain the version of the tool
Tool Description Homepage
crabs Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses https://github.com/gjeunen/reference_database_creator
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:11:41 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fcrabs%2Fimport/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/crabs/import/blobs/sha256:a5552aa15acd003b5495501f9d9f94ee6b804a4faac59fd9d1394c1bebe88d2d
Size 2.9 KB
Checksum sha256:a5552aa15acd003b5495501f9d9f94ee6b804a4faac59fd9d1394c1bebe88d2d
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:11:41 (UTC) 3 2.9 KB
0.0.0-3fc6d40 22 Apr 2026 15:08:06 (UTC) 3 3.0 KB
0.0.0-0c7146d 08 Apr 2026 18:54:34 (UTC) 2 2.9 KB