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:false ]

`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:false ]

`${prefix}.bam`
`:file`

Merged BAM file

*.bam

`bam_index`

`meta`
`:map`

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

`*.bai`
`:file`

BAM index file

*.bai

`checksum`

`meta`
`:map`

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

`*.md5`
`:file`

Checksum file

*.md5

`versions_biobambam`

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

The name of the process

`biobambam`
`:string`

The name of the tool

`bammerge --version |& sed '1!d; 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

`biobambam`
`:string`

The name of the tool

`bammerge --version |& sed '1!d; s/.*version //; s/.\$//'`
`:eval`

The expression to obtain the version of the tool

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_biobambam`

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

`biobambam`
`:string`

`bammerge --version |& sed '1!d; s/.*version //; s/.\$//'`
`:eval`

Topics

`versions`

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

`biobambam`
`:string`

`bammerge --version |& sed '1!d; s/.*version //; s/.\$//'`
`:eval`

Tools

biobambam
GPL v3

maintainer

get in touch

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_biobambam

${task.process}:string

biobambam:string

bammerge --version |& sed '1!d; s/.*version //; s/.\$//':eval

Topics

versions

${task.process}:string

biobambam:string

bammerge --version |& sed '1!d; s/.*version //; s/.\$//':eval

Tools

biobambam GPL v3

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`bam_index`

`meta`
`:map`

`*.bai`
`:file`

`checksum`

`meta`
`:map`

`*.md5`
`:file`

`versions_biobambam`

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

`biobambam`
`:string`

`bammerge --version |& sed '1!d; s/.*version //; s/.\$//'`
`:eval`

`versions`

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

`biobambam`
`:string`

`bammerge --version |& sed '1!d; s/.*version //; s/.\$//'`
`:eval`

biobambam
GPL v3