modules/mitohifi_mitohifi

A python workflow that assembles mitogenomes from Pacbio HiFi reads

mitochondrionchloroplastPacBio

https://github.com/nf-core/modules/[...]/modules/nf-core/mitohifi/mitohifi

Description

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`input`
`:file`

Path to PacBio HiFi reads or fasta contigs

*.{fa,fa.gz,fasta,fasta.gz}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`ref_fa`
`:file`

Reference mitochondrial genome to align reads or contigs against

*.{fa,fasta}

`ref_gb`
`:file`

Reference mitochondrial genome annotation

*.{gb}

`input_mode`
`:string`

Specifies type of input - reads or contigs

{reads,contigs}

`mito_code`
`:integer`

Integer reference number of mitochondrial genetic code - see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details.

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome.fasta`
`:file`

Fasta file containing final chosen mitochondrial sequence

final_mitogenome.fasta

`stats`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`contigs_stats.tsv`
`:file`

Statistics of all identified mitochondrial contigs

contigs_stats.tsv

`gb`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome.gb`
`:file`

GB annotation file of final chosen mitochondrial sequence, if Mitofinder mode was used for annotation.

final_mitogenome.gb

`gff`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome.gff`
`:file`

GB annotation file of final chosen mitochondrial sequence, if Mitos mode was used for annotation.

final_mitogenome.gff

`all_potential_contigs`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`all_potential_contigs.fa`
`:file`

Fasta file containing sequences of all potential mitogenome contigs

all_potential_contigs.fa

`contigs_annotations`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`contigs_annotations.png`
`:file`

Graphical representation of annotated genes and tRNAs

contigs_annotations.png

`contigs_circularization`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`contigs_circularization/`
`:directory`

Contains circularization reports

contigs_circularization/

`contigs_filtering`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`contigs_filtering/`
`:directory`

Contains files with initial blast matches

contigs_filtering/

`coverage_mapping`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`coverage_mapping/`
`:directory`

Contains statistics on coverage mapping

coverage_mapping/

`coverage_plot`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`coverage_plot.png`
`:file`

Read coverage plot for mitochondrial contigs

coverage_plot.png

`final_mitogenome_annotation`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome.annotation.png`
`:file`

Graphical representation of annotated genes for the final mitogenome contig

final_mitogenome.annotation.png

`final_mitogenome_choice`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome_choice/`
`:directory`

Files with potential contigs clusterings and alignments

final_mitogenome_choice/

`final_mitogenome_coverage`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`final_mitogenome.coverage.png`
`:file`

Graphical representation of reads coverage plot for the final mitogenome contig

final_mitogenome.coverage.png

`potential_contigs`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`potential_contigs/`
`:directory`

Files with sequences and annotations of the potential contigs

potential_contigs/

`reads_mapping_and_assembly`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`reads_mapping_and_assembly/`
`:directory`

Read mapping files for run from the raw reads

reads_mapping_and_assembly/

`shared_genes`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`shared_genes.tsv`
`:directory`

Report on genes shared with the reference genome

shared_genes.tsv

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.log`
`:directory`

Log file describing Mitohifi run

*.log

`all_files`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*`
`:file`

All files output by Mitohifi in a single channel.

`versions_mitohifi`

`${task.process}`
`:string`

Name of the process

`mitohifi`
`:string`

The name of the tool

`echo 3.2.3`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

Name of the process

`mitohifi`
`:string`

The name of the tool

`echo 3.2.3`
`:eval`

The expression to obtain the version of the tool

Tools

mitohifi.py
MIT

A python workflow that assembles mitogenomes from Pacbio HiFi reads

github.com/marcelauliano/MitoHiFi 10.1101/2022.12.23.521667

modules/mitohifi_mitohifi

Description

Input

meta:map

input:file

meta2:map

ref_fa:file

ref_gb:file

input_mode:string

mito_code:integer

Output

fasta

meta:map

final_mitogenome.fasta:file

stats

meta:map

contigs_stats.tsv:file

gb

meta:map

final_mitogenome.gb:file

gff

meta:map

final_mitogenome.gff:file

all_potential_contigs

meta:map

all_potential_contigs.fa:file

contigs_annotations

meta:map

contigs_annotations.png:file

contigs_circularization

meta:map

contigs_circularization/:directory

contigs_filtering

meta:map

contigs_filtering/:directory

coverage_mapping

meta:map

coverage_mapping/:directory

coverage_plot

meta:map

coverage_plot.png:file

final_mitogenome_annotation

meta:map

final_mitogenome.annotation.png:file

final_mitogenome_choice

meta:map

final_mitogenome_choice/:directory

final_mitogenome_coverage

meta:map

final_mitogenome.coverage.png:file

potential_contigs

meta:map

potential_contigs/:directory

reads_mapping_and_assembly

meta:map

reads_mapping_and_assembly/:directory

shared_genes

meta:map

shared_genes.tsv:directory

log

meta:map

*.log:directory

all_files

meta:map

*:file

versions_mitohifi

${task.process}:string

mitohifi:string

echo 3.2.3:eval

Topics

versions

${task.process}:string

mitohifi:string

echo 3.2.3:eval

Tools

mitohifi.py MIT

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`meta2`
`:map`

`ref_fa`
`:file`

`ref_gb`
`:file`

`input_mode`
`:string`

`mito_code`
`:integer`

`fasta`

`meta`
`:map`

`final_mitogenome.fasta`
`:file`

`stats`

`meta`
`:map`

`contigs_stats.tsv`
`:file`

`gb`

`meta`
`:map`

`final_mitogenome.gb`
`:file`

`gff`

`meta`
`:map`

`final_mitogenome.gff`
`:file`

`all_potential_contigs`

`meta`
`:map`

`all_potential_contigs.fa`
`:file`

`contigs_annotations`

`meta`
`:map`

`contigs_annotations.png`
`:file`

`contigs_circularization`

`meta`
`:map`

`contigs_circularization/`
`:directory`

`contigs_filtering`

`meta`
`:map`

`contigs_filtering/`
`:directory`

`coverage_mapping`

`meta`
`:map`

`coverage_mapping/`
`:directory`

`coverage_plot`

`meta`
`:map`

`coverage_plot.png`
`:file`

`final_mitogenome_annotation`

`meta`
`:map`

`final_mitogenome.annotation.png`
`:file`

`final_mitogenome_choice`

`meta`
`:map`

`final_mitogenome_choice/`
`:directory`

`final_mitogenome_coverage`

`meta`
`:map`

`final_mitogenome.coverage.png`
`:file`

`potential_contigs`

`meta`
`:map`

`potential_contigs/`
`:directory`

`reads_mapping_and_assembly`

`meta`
`:map`

`reads_mapping_and_assembly/`
`:directory`

`shared_genes`

`meta`
`:map`

`shared_genes.tsv`
`:directory`

`log`

`meta`
`:map`

`*.log`
`:directory`

`all_files`

`meta`
`:map`

`*`
`:file`

`versions_mitohifi`

`${task.process}`
`:string`

`mitohifi`
`:string`

`echo 3.2.3`
`:eval`

`versions`

`${task.process}`
`:string`

`mitohifi`
`:string`

`echo 3.2.3`
`:eval`

mitohifi.py
MIT