modules/pmdtools_filter

pmdtools command to filter ancient DNA molecules from others

pmdtoolsaDNAfilterdamage

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

Description

pmdtools command to filter ancient DNA molecules from others

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file

*.bam

`bai`
`:file`

BAM index file

*.bai

`threshold`
`:float`

Post-mortem damage score threshold

`reference`
`:file`

FASTA file

*.{fa,fasta}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Filtered BAM file

*.bam

`versions_pmdtools`

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

The name of the process

`pmdtools`
`:string`

The name of the tool

`pmdtools --version | sed 's/.*v//'`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;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

`pmdtools`
`:string`

The name of the tool

`pmdtools --version | sed 's/.*v//'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

pmdtools
GPL v3

Compute postmortem damage patterns and decontaminate ancient genomes

github.com/pontussk/PMDtools 10.1073/pnas.1318934111

modules/pmdtools_filter

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`threshold`
`:float`

`reference`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_pmdtools`

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

`pmdtools`
`:string`

`pmdtools --version | sed 's/.*v//'`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Topics

`versions`

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

`pmdtools`
`:string`

`pmdtools --version | sed 's/.*v//'`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Tools

pmdtools
GPL v3

maintainer

get in touch

modules/pmdtools_filter

Description

Input

meta :map

bam :file

bai :file

threshold :float

reference :file

Output

bam

meta :map

*.bam :file

versions_pmdtools

${task.process} :string

pmdtools :string

pmdtools --version | sed 's/.*v//' :eval

versions_samtools

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Topics

versions

${task.process} :string

pmdtools :string

pmdtools --version | sed 's/.*v//' :eval

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Tools

pmdtoolsGPL v3

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`threshold`
`:float`

`reference`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_pmdtools`

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

`pmdtools`
`:string`

`pmdtools --version | sed 's/.*v//'`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`pmdtools`
`:string`

`pmdtools --version | sed 's/.*v//'`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

pmdtools
GPL v3