modules/bbmap_pileup

Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.

fastagenomecoverage

https://github.com/nf-core/modules/[...]/modules/nf-core/bbmap/pileup

Description

Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.

Input

name:type

description

pattern

`meta:map`

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

]

`bam:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

Output

name:type

description

pattern

`covstats`

`meta:map`

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

]

`*.stats.txt:file`

Coverage statistics

*.stats.txt

`hist`

`meta:map`

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

]

`*.hist.txt:file`

Histogram of # occurrences of each depth level

*.hist.txt

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

bbmap
UC-LBL license (see package)

BBMap is a short read aligner, as well as various other bioinformatic tools.

jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh

modules/bbmap_pileup

Description

Input

`meta:map`

`bam:file`

Output

`covstats`

`meta:map`

`*.stats.txt:file`

`hist`

`meta:map`

`*.hist.txt:file`

`versions`

`versions.yml:file`

Tools

bbmap
UC-LBL license (see package)

included in

maintainer

get in touch

modules/bbmap_pileup

Description

Input

meta:map

bam:file

Output

covstats

meta:map

*.stats.txt:file

hist

meta:map

*.hist.txt:file

versions

versions.yml:file

Tools

bbmap UC-LBL license (see package)

included in

maintainer

get in touch

`meta:map`

`bam:file`

`covstats`

`meta:map`

`*.stats.txt:file`

`hist`

`meta:map`

`*.hist.txt:file`

`versions`

`versions.yml:file`

bbmap
UC-LBL license (see package)