modules/biobambam_bammerge

Merge a list of sorted bam files

mergebamsorted

https://github.com/nf-core/modules/[...]/modules/nf-core/biobambam/bammerge

Description

Merge a list of sorted bam files

Input

name:type

description

pattern

`meta:map`

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

]

`bam:file`

List containing 1 or more bam files

Output

name:type

description

pattern

`bam`

`meta:map`

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

]

`${prefix}.bam:file`

Merged BAM file

*.bam

`bam_index`

`meta:map`

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

]

`*.bai:file`

BAM index file

*

`checksum`

`meta:map`

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

]

`*.md5:file`

Checksum file

*

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

biobambam
GPL v3

biobambam is a set of tools for early stage alignment file processing.

gitlab.com/german.tischler/biobambam2 gitlab.com/german.tischler/biobambam2/-/blob/master/README.md 10.1186/1751-0473-9-13

modules/biobambam_bammerge

Description

Input

meta:map

bam:file

Output

bam

meta:map

${prefix}.bam:file

bam_index

meta:map

*.bai:file

checksum

meta:map

*.md5:file

versions

versions.yml:file

Tools

biobambam GPL v3

`meta:map`

`bam:file`

`bam`

`meta:map`

`${prefix}.bam:file`

`bam_index`

`meta:map`

`*.bai:file`

`checksum`

`meta:map`

`*.md5:file`

`versions`

`versions.yml:file`

biobambam
GPL v3