samtools/samtools_faidx
idex
fasta
faidx
Description
Indexes FASTA files to enable random access to fasta and fastq files.
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. |
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. |
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. |
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 Relationships
Used by
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Current component
samtools/samtools_faidxbiobox v0.1.0
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