modules/hifitrimmer_processblast

Run hifi_trimmer process_blast to process a BLAST search of adapter sequences against PacBio HiFi reads. Primary output is a BED describing regions to exclude, a json of summary information, and an optional hits file.

pacbiobamhifi_trimmerprocessblastquality controladapter removal

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

Description

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`blast`
`:file`

BLAST TSV output file used by hifi_trimmer (e.g. .blast, .out). Must be generated using “blastn -query -db <adapter_db> -outfmt ‘6 std qlen’”.

*.{blast,out}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`yaml`
`:file`

YAML file contain trimming/filtering configuration for hifi_trimmer

*.{yaml,yml}

Output

name:type

description

pattern

`bed`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.bed.gz`
`:file`

Gzipped BED file of selected reads

*.bed.gz

`summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.summary.json`
`:file`

JSON summary including trimming and filtering information

*.summary.json

`hits`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.hits`
`:file`

Optional hits file produced by hifi_trimmer (may be absent when no hits found or ‘-hf’ is not specified)

*.hits

`versions_hifitrimmer`

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

The name of the process

`hifi-trimmer`
`:string`

The name of the tool

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`hifi-trimmer`
`:string`

The name of the tool

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

The expression to obtain the version

Tools

hifi-trimmer
MIT

hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming BAM files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.

github.com/sanger-tol/hifi-trimmer

modules/hifitrimmer_processblast

Description

Input

`meta`
`:map`

`blast`
`:file`

`meta2`
`:map`

`yaml`
`:file`

Output

`bed`

`meta`
`:map`

`*.bed.gz`
`:file`

`summary`

`meta`
`:map`

`*.summary.json`
`:file`

`hits`

`meta`
`:map`

`*.hits`
`:file`

`versions_hifitrimmer`

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

`hifi-trimmer`
`:string`

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

Topics

`versions`

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

`hifi-trimmer`
`:string`

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

Tools

hifi-trimmer
MIT

maintainer

get in touch

modules/hifitrimmer_processblast

Description

Input

meta :map

blast :file

meta2 :map

yaml :file

Output

bed

meta :map

*.bed.gz :file

summary

meta :map

*.summary.json :file

hits

meta :map

*.hits :file

versions_hifitrimmer

${task.process} :string

hifi-trimmer :string

hifi-trimmer --version | cut -d' ' -f3 :eval

Topics

versions

${task.process} :string

hifi-trimmer :string

hifi-trimmer --version | cut -d' ' -f3 :eval

Tools

hifi-trimmerMIT

maintainer

get in touch

`meta`
`:map`

`blast`
`:file`

`meta2`
`:map`

`yaml`
`:file`

`bed`

`meta`
`:map`

`*.bed.gz`
`:file`

`summary`

`meta`
`:map`

`*.summary.json`
`:file`

`hits`

`meta`
`:map`

`*.hits`
`:file`

`versions_hifitrimmer`

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

`hifi-trimmer`
`:string`

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

`versions`

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

`hifi-trimmer`
`:string`

`hifi-trimmer --version | cut -d' ' -f3`
`:eval`

hifi-trimmer
MIT