modules/pbmarkdup

Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes duplicates.

markdupbamfastqfasta

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

Description

Takes one or multiple sequencing chips of an amplified library as HiFi reads and marks or removes duplicates.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`input`
`:file`

Sequencing reads in BAM, FASTQ, or FASTA format.

*.{bam,f*a,/.*f.*\.gz/}

Output

name:type

description

pattern

`markduped`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

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

Markduplicated sequencing reads in the same format as the input file.

*.{bam,f*a,/.*f.*\.gz/}

`dupfile`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${dupfile_name}`
`:file`

(Optional) File listing duplicate reads (Specify by –dup-file).

*.{bam,f*a,/.*f.*\.gz/}

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.pbmarkdup.log`
`:file`

Log file generated by pbmarkdup (if –log-level is specified).

*.pbmarkdup.log

`versions_pbmarkdup`

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

Name of the process

`pbmarkdup`
`:string`

The name of the tool

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

Name of the process

`pbmarkdup`
`:string`

The name of the tool

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

The expression to obtain the version of the tool

Tools

pbmarkdup
BSD-3-Clause

pbmarkdup identifies and marks duplicate reads in PacBio HiFi (CCS) data. It clusters highly similar CCS reads to detect PCR duplicates and flags them in the output files (BAM,FASTQ,FASTA) (duplicate bit 0x400), optionally removing duplicates. (duplicate bit 0x400), optionally removing duplicates.

github.com/PacificBiosciences/pbmarkdup

modules/pbmarkdup

Description

Input

`meta`
`:map`

`input`
`:file`

Output

`markduped`

`meta`
`:map`

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

`dupfile`

`meta`
`:map`

`${dupfile_name}`
`:file`

`log`

`meta`
`:map`

`*.pbmarkdup.log`
`:file`

`versions_pbmarkdup`

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

`pbmarkdup`
`:string`

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

Topics

`versions`

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

`pbmarkdup`
`:string`

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

Tools

pbmarkdup
BSD-3-Clause

maintainer

get in touch

modules/pbmarkdup

Description

Input

meta :map

input :file

Output

markduped

meta :map

${prefix}.${suffix} :file

dupfile

meta :map

${dupfile_name} :file

log

meta :map

*.pbmarkdup.log :file

versions_pbmarkdup

${task.process} :string

pbmarkdup :string

pbmarkdup --version | cut -d' ' -f2 :eval

Topics

versions

${task.process} :string

pbmarkdup :string

pbmarkdup --version | cut -d' ' -f2 :eval

Tools

pbmarkdupBSD-3-Clause

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`markduped`

`meta`
`:map`

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

`dupfile`

`meta`
`:map`

`${dupfile_name}`
`:file`

`log`

`meta`
`:map`

`*.pbmarkdup.log`
`:file`

`versions_pbmarkdup`

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

`pbmarkdup`
`:string`

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

`versions`

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

`pbmarkdup`
`:string`

`pbmarkdup --version | cut -d' ' -f2`
`:eval`

pbmarkdup
BSD-3-Clause