Description

Compress and index a Fasta file in multiple formats

Input

Name
Description
Pattern

ch_fasta (file)

Structure [ val(meta), path(fasta) ] Meta is the Groovy Map containing sample information

val_run_samtools_dict (boolean)

Boolean flag to control creation of the SAMtools sequence dictionary. If true, the samtools dict component is run; if false, no dictionary is generated.

Output

Name
Description
Pattern

fasta_gz (file)

Structure: [ val(meta), path(genome.fa.gz) ] Input Fasta file compressed with bgzip

faidx (file)

Structure: [ val(meta), path(genome.fa.gz.fai) ] Samtools faidx index of the Fasta file

dict (file)

Structure: [ val(meta), path(genome.fa.gz.dict) ] Samtools sequence dictionary of the Fasta file (if requested)

gzi (file)

Structure: [ val(meta), path(genome.fa.gz.gzi) ] Bgzip index of the Fasta file

sizes (file)

Structure: [ val(meta), path(genome.fa.gz.sizes) ] TSV file of all sequences and their sizes

Components

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