modules/bamutil_trimbam

trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping

bamtrimclippingbamUtiltrimBam

https://github.com/nf-core/modules/[...]/modules/nf-core/bamutil/trimbam

Description

trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file

*.bam

`trim_left`
`:integer`

Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.

`trim_right`
`:integer`

Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Trimmed but unsorted BAM file

*.bam

`versions_bamutil`

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

The name of the process

`bamutil`
`:string`

The name of the tool

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`bamutil`
`:string`

The name of the tool

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

The expression to obtain the version of the tool

Tools

bamutil
GPL v3

Programs that perform operations on SAM/BAM files, all built into a single executable, bam.

genome.sph.umich.edu/wiki/BamUtil genome.sph.umich.edu/wiki/BamUtil:_trimBam https://github.com/statgen/bamUtil 10.1101/gr.176552.114

modules/bamutil_trimbam

Description

Input

`meta`
`:map`

`bam`
`:file`

`trim_left`
`:integer`

`trim_right`
`:integer`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_bamutil`

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

`bamutil`
`:string`

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

Topics

`versions`

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

`bamutil`
`:string`

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

Tools

bamutil
GPL v3

maintainer

get in touch

modules/bamutil_trimbam

Description

Input

meta:map

bam:file

trim_left:integer

trim_right:integer

Output

bam

meta:map

*.bam:file

versions_bamutil

${task.process}:string

bamutil:string

bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//':eval

Topics

versions

${task.process}:string

bamutil:string

bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//':eval

Tools

bamutil GPL v3

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`trim_left`
`:integer`

`trim_right`
`:integer`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_bamutil`

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

`bamutil`
`:string`

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

`versions`

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

`bamutil`
`:string`

`bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'`
`:eval`

bamutil
GPL v3