samtools/samtools_faidx

idex

fasta

faidx

Description

Indexes FASTA files to enable random access to fasta and fastq files.

Type

bash_script

License

MIT/Expat

Keywords

idex

fasta

faidx

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
length: [ 60 ]  
output: "$id.$key.output.fasta"  
mark_strand: [ "rc" ]  
fai_idx: "$id.$key.fai_idx.fai"  
gzi_idx: "$id.$key.gzi_idx.gzi"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/samtools/samtools_faidx/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file	FASTA input file.
--length -n	integer	Length for FASTA sequence line wrapping. If zero, this means do not line wrap. Defaults to the line length in the input file.
--region_file -r	file	File of regions. Format is chr:from-to. One per line. Must be used with --output to avoid sending output to stdout.

Name

Type & Properties

--input

file

--length

-n

integer

--region_file

-r

file

Options

Name	Type & Properties	Description
--continue	boolean_true	Continue working if a non-existent region is requested.
--reverse_complement -i	boolean_true	Reverse complement sequences.

Name

Type & Properties

--continue

boolean_true

--reverse_complement

-i

boolean_true

Outputs

Name	Type & Properties	Description
--output -o	file required output	Write output to file.
--mark_strand	string	Add strand indicator to sequence name. Options are: [ rc, no, sign, custom,<pos>,<neg> ]
--fai_idx	file output	Read/Write to specified index file (default file.fa.fai).
--gzi_idx	file output	Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).
--fastq	boolean_true	Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.

Name

Type & Properties

--output

-o

file

required

output

--mark_strand

string

--fai_idx

file

output

--gzi_idx

file

output

--fastq

boolean_true