modules/hifitrimmer_trim

Run hifi-trimmer trim to filter and trim adapter-hit regions from PacBio HiFi reads. Supports BAM/CRAM/FASTA/FASTQ input and emits gzip-compressed FASTA (default) or FASTQ, or SAM, BAM, or CRAM according to the selected output format.

pacbiobamfastafastqhifi_trimmerfilteringtrimmingquality controladapter removal

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

Input BAM/CRAM/FASTA/FASTQ file to filter and trim

*.{bam,cram,fa,fasta,fa.gz,fasta.gz,fastq,fq,fastq.gz,fq.gz}

`bed`
`:file`

Input gzipped bed file contains regions to filter/trim

*.bed.gz

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`${prefix}.fasta.gz`
`:file`

Gzip-compressed FASTA output from hifi-trimmer (default format)

*.fasta.gz

`fastq`

`meta`
`:map`

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

`${prefix}.fastq.gz`
`:file`

Gzip-compressed FASTQ output from hifi-trimmer when -f fastq is selected

*.fastq.gz

`sam`

`meta`
`:map`

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

`${prefix}.sam`
`:file`

SAM output from hifi-trimmer when -f sam is selected

*.sam

`bam`

`meta`
`:map`

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

`${prefix}.bam`
`:file`

BAM output from hifi-trimmer (default format)

*.bam

`cram`

`meta`
`:map`

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

`${prefix}.cram`
`:file`

CRAM output from hifi-trimmer when -f cram is selected

*.cram

`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 read files.

github.com/sanger-tol/hifi-trimmer

modules/hifitrimmer_trim

Description

Input

`meta`
`:map`

`input`
`:file`

`bed`
`:file`

Output

`fasta`

`meta`
`:map`

`${prefix}.fasta.gz`
`:file`

`fastq`

`meta`
`:map`

`${prefix}.fastq.gz`
`:file`

`sam`

`meta`
`:map`

`${prefix}.sam`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`: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_trim

Description

Input

meta :map

input :file

bed :file

Output

fasta

meta :map

${prefix}.fasta.gz :file

fastq

meta :map

${prefix}.fastq.gz :file

sam

meta :map

${prefix}.sam :file

bam

meta :map

${prefix}.bam :file

cram

meta :map

${prefix}.cram :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`

`input`
`:file`

`bed`
`:file`

`fasta`

`meta`
`:map`

`${prefix}.fasta.gz`
`:file`

`fastq`

`meta`
`:map`

`${prefix}.fastq.gz`
`:file`

`sam`

`meta`
`:map`

`${prefix}.sam`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`: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