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

]

`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

]

`*.bam:file`

Trimmed but unsorted BAM file

*.bam

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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`

`versions.yml:file`

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

versions.yml:file

Tools

bamutil GPL v3

maintainer

get in touch

`meta:map`

`bam:file`

`trim_left:integer`

`trim_right:integer`

`bam`

`meta:map`

`*.bam:file`

`versions`

`versions.yml:file`

bamutil
GPL v3