modules/artic_aligntrim

Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.

articprimer trimmingamplicongenomicssequencingnanoporeillumina

https://github.com/nf-core/modules/[...]/modules/nf-core/artic/aligntrim

Description

Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.

Input

name:type

description

pattern

`meta`
`:map`

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

`samfile`
`:file`

BAM or SAM file containing aligned reads

*.{bam,sam}

`scheme_bed`
`:file`

BED file containing amplicon scheme primer locations

*.bed

`normalise_depth`
`:integer`

Normalise the read depth to this value

`sort_bam`
`:boolean`

Optionally sort the BAM file after trimming

Output

name:type

description

pattern

`primertrimmed_bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`.primertrimmed.bam`
`:file`

BAM file with primer sequences soft clipped

*.primertrimmed*.bam

`align_trim_report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.align_trim_report.tsv`
`:file`

TSV report containing full details of primer trimming for each read / read pair

*.align_trim_report.tsv

`amp_depth_report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.amp_depth_report.tsv`
`:file`

TSV report containing mean depth per amplicon

*.amp_depth_report.tsv

`versions_align_trim`

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

The name of the process

`align_trim`
`:string`

The name of the tool

`align_trim --version | sed 's/align_trim //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`align_trim`
`:string`

The name of the tool

`align_trim --version | sed 's/align_trim //'`
`:eval`

The expression to obtain the version of the tool

Tools

align_trim
MIT

ARTIC align_trim: A tool for trimming amplicon sequencing primers from aligned reads.

github.com/artic-network/align_trim github.com/artic-network/align_trim/blob/master/README.md https://github.com/artic-network/align_trim

modules/artic_aligntrim

Description

Input

`meta`
`:map`

`samfile`
`:file`

`scheme_bed`
`:file`

`normalise_depth`
`:integer`

`sort_bam`
`:boolean`

Output

`primertrimmed_bam`

`meta`
`:map`

`.primertrimmed.bam`
`:file`

`align_trim_report`

`meta`
`:map`

`*.align_trim_report.tsv`
`:file`

`amp_depth_report`

`meta`
`:map`

`*.amp_depth_report.tsv`
`:file`

`versions_align_trim`

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

`align_trim`
`:string`

`align_trim --version | sed 's/align_trim //'`
`:eval`

Topics

`versions`

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

`align_trim`
`:string`

`align_trim --version | sed 's/align_trim //'`
`:eval`

Tools

align_trim
MIT

maintainer

get in touch

modules/artic_aligntrim

Description

Input

meta:map

samfile:file

scheme_bed:file

normalise_depth:integer

sort_bam:boolean

Output

primertrimmed_bam

meta:map

*.primertrimmed*.bam:file

align_trim_report

meta:map

*.align_trim_report.tsv:file

amp_depth_report

meta:map

*.amp_depth_report.tsv:file

versions_align_trim

${task.process}:string

align_trim:string

align_trim --version | sed 's/align_trim //':eval

Topics

versions

${task.process}:string

align_trim:string

align_trim --version | sed 's/align_trim //':eval

Tools

align_trim MIT

maintainer

get in touch

`meta`
`:map`

`samfile`
`:file`

`scheme_bed`
`:file`

`normalise_depth`
`:integer`

`sort_bam`
`:boolean`

`primertrimmed_bam`

`meta`
`:map`

`.primertrimmed.bam`
`:file`

`align_trim_report`

`meta`
`:map`

`*.align_trim_report.tsv`
`:file`

`amp_depth_report`

`meta`
`:map`

`*.amp_depth_report.tsv`
`:file`

`versions_align_trim`

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

`align_trim`
`:string`

`align_trim --version | sed 's/align_trim //'`
`:eval`

`versions`

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

`align_trim`
`:string`

`align_trim --version | sed 's/align_trim //'`
`:eval`

align_trim
MIT