Nextflow Registry | nf-core/chewbbaca/allelecall@0.0.0-6c4ed3a

nf-core/chewbbaca/allelecall @ 0.0.0-6c4ed3a

Determine the allelic profiles of a genome using a pre-defined schema

cgMLST WGS genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @anwarMZ

Determine the allelic profiles of a genome using a pre-defined schema

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

include { CHEWBBACA_ALLELECALL } from 'nf-core/chewbbaca/allelecall'

MIT License

Process

`Name`	`CHEWBBACA_ALLELECALL`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`fasta` file	FASTA file(s) to be staged in a directory for allele calling `*.{fasta,fa,fna}`

#2 tuple

`meta2` map	Groovy Map containing scheme information e.g. `[ id:'scheme' ]`
`scheme` directory	Directory containing the schema files `*/`

Output 10 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_logging_info.txt` file	File contains the log information `*_logging_info.txt`

#2 stats tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_results_statistics.tsv` file	File contains the total number of exact matches `*_results_statistics.tsv`

#3 alleles tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_results_alleles.tsv` file	File contains the allelic profiles determined for the input sample `*_results_alleles.tsv`

#4 invalid_cds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_invalid_cds.txt` file	File contains the list of alleles predicted by Prodigal that were excluded `*_invalid_cds.txt`

#5 contigs_info tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_results_contigsInfo.tsv` file	File contains the loci coordinates in the genomes analyzed `*_results_contigsInfo.tsv`

#6 cds_coordinates tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_cds_coordinates.tsv` file	File contains the coordinates of the CDS in the input sample `*_cds_coordinates.tsv`

#7 paralogous_loci tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_paralogous_loci.tsv` file	File contains the sets of paralogous loci identified in the input sample `*_paralogous_loci.tsv`

#8 paralogous_counts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_paralogous_counts.tsv` file	File contains the list of paralogous loci and the number of times those loci matched a CDS that was also similar to other loci in the schema `*_paralogous_counts.tsv`

#9 loci_summary_stats tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*_loci_summary_stats.tsv` file	File contains summary statistics for each locus `*_loci_summary_stats.tsv`

#10 versions_chewbbaca tuple

`${task.process}` string	The name of the process
`chewbbaca` string	The name of the tool
`chewie --version 2>&1 \| sed 's/chewBBACA version: //'` eval	The expression to obtain the version of the tool