modules/biobambam_bamsormadup

Parallel sorting and duplicate marking

markduplicatessortbamcram

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

Description

Parallel sorting and duplicate marking

Input

name:type

description

pattern

`meta`
`:map`

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

`bams`
`:file`

List containing 1 or more bam files

`meta2`
`:map`

Groovy Map containing genome information e.g. [ id:‘genome’ ]

`fasta`
`:file`

Reference genome in FASTA format (optional)

*.{fa,fasta,fna}

`fai`
`:file`

Reference genome in FASTA index format (optional)

*.{fai}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

BAM file with duplicate reads marked/removed

*.bam

`bam_index`

`meta`
`:map`

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

`*.bam.bai`
`:file`

BAM index file

*.bai

`cram`

`meta`
`:map`

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

`*.cram`
`:file`

CRAM file with duplicate reads marked/removed

*.cram

`metrics`

`meta`
`:map`

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

`*.metrics.txt`
`:file`

Duplicate metrics file generated by biobambam

*.{metrics.txt}

`versions_biobambam`

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

The name of the process

`biobambam`
`:string`

The name of the tool

`bamsormadup --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

`bamsormadup --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_bamsormadup

Description

Input

`meta`
`:map`

`bams`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bam_index`

`meta`
`:map`

`*.bam.bai`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`metrics`

`meta`
`:map`

`*.metrics.txt`
`:file`

`versions_biobambam`

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

`biobambam`
`:string`

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

Topics

`versions`

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

`biobambam`
`:string`

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

Tools

biobambam
GPL v3

maintainer

get in touch

modules/biobambam_bamsormadup

Description

Input

meta:map

bams:file

meta2:map

fasta:file

fai:file

Output

bam

meta:map

*.bam:file

bam_index

meta:map

*.bam.bai:file

cram

meta:map

*.cram:file

metrics

meta:map

*.metrics.txt:file

versions_biobambam

${task.process}:string

biobambam:string

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

Topics

versions

${task.process}:string

biobambam:string

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

Tools

biobambam GPL v3

maintainer

get in touch

`meta`
`:map`

`bams`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bam_index`

`meta`
`:map`

`*.bam.bai`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`metrics`

`meta`
`:map`

`*.metrics.txt`
`:file`

`versions_biobambam`

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

`biobambam`
`:string`

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

`versions`

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

`biobambam`
`:string`

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

biobambam
GPL v3