modules/pbbam_pbmerge

The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.

pbbampbmergebam

https://github.com/nf-core/modules/[...]/modules/nf-core/pbbam/pbmerge

This module is deprecated.

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM files to merge

*.bam

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

The merged bam file

*.bam

`pbi`

`meta`
`:map`

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

`*.pbi`
`:file`

BAM Pacbio index file

*.bam.pbi

`versions_pbbam`

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

The name of the process

`pbbam`
`:string`

The name of the tool

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pbbam`
`:string`

The name of the tool

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

The expression to obtain the version of the tool

Tools

pbbam
BSD-3-Clause-Clear

PacBio BAM C++ library

github.com/PacificBiosciences/pbbioconda pbbam.readthedocs.io/en/latest/tools/pbmerge https://github.com/pacificbiosciences/pbbam/

modules/pbbam_pbmerge

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`pbi`

`meta`
`:map`

`*.pbi`
`:file`

`versions_pbbam`

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

`pbbam`
`:string`

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

Topics

`versions`

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

`pbbam`
`:string`

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

Tools

pbbam
BSD-3-Clause-Clear

maintainer

get in touch

modules/pbbam_pbmerge

Description

Input

meta :map

bam :file

Output

bam

meta :map

*.bam :file

pbi

meta :map

*.pbi :file

versions_pbbam

${task.process} :string

pbbam :string

pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//' :string

Topics

versions

${task.process} :string

pbbam :string

pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//' :string

Tools

pbbamBSD-3-Clause-Clear

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`pbi`

`meta`
`:map`

`*.pbi`
`:file`

`versions_pbbam`

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

`pbbam`
`:string`

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

`versions`

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

`pbbam`
`:string`

`pbmerge --version | head -n1 | sed 's/pbmerge //' | sed -E 's/ .+//'`
`:string`

pbbam
BSD-3-Clause-Clear