modules/authentict_deam2cont

Use deamination patterns to estimate contamination in single-stranded libraries

authentictancientDNAsingle-strandeddeaminationcontaminationdamage

https://github.com/nf-core/modules/[...]/modules/nf-core/authentict/deam2cont

Description

Use deamination patterns to estimate contamination in single-stranded libraries

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file (Mandatory)

*.{bam,cram,sam}

`meta2`
`:map`

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

`config`
`:file`

Optional AuthentiCT configuration text file

*

`meta3`
`:map`

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

`positions`
`:file`

Optional text file with positions that sequences should overlap

*

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.txt`
`:file`

Maximum likelihood estimates with associated standard errors

*.txt

`versions_authentict`

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

The name of the process

`authentict`
`:string`

The name of the tool

`echo \$(AuthentiCT --version 2>&1)`
`: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 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`authentict`
`:string`

The name of the tool

`echo \$(AuthentiCT --version 2>&1)`
`: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 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

Tools

authentict
GPL v3

Estimates present-day DNA contamination in ancient DNA single-stranded libraries.

github.com/StephanePeyregne/AuthentiCT 10.1186/s13059-020-02123-y

modules/authentict_deam2cont

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`config`
`:file`

`meta3`
`:map`

`positions`
`:file`

Output

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_authentict`

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

`authentict`
`:string`

`echo \$(AuthentiCT --version 2>&1)`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

Topics

`versions`

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

`authentict`
`:string`

`echo \$(AuthentiCT --version 2>&1)`
`:eval`

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

`samtools`
`:string`

`samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

Tools

authentict
GPL v3

maintainers

get in touch

modules/authentict_deam2cont

Description

Input

meta:map

bam:file

meta2:map

config:file

meta3:map

positions:file

Output

txt

meta:map

*.txt:file

versions_authentict

${task.process}:string

authentict:string

echo \$(AuthentiCT --version 2>&1):eval

versions_samtools

${task.process}:string

samtools:string

samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //':eval

Topics

versions

${task.process}:string

authentict:string

echo \$(AuthentiCT --version 2>&1):eval

${task.process}:string

samtools:string

samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //':eval

Tools

authentict GPL v3

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`config`
`:file`

`meta3`
`:map`

`positions`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_authentict`

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

`authentict`
`:string`

`echo \$(AuthentiCT --version 2>&1)`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

`versions`

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

`authentict`
`:string`

`echo \$(AuthentiCT --version 2>&1)`
`:eval`

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

`samtools`
`:string`

`samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'`
`:eval`

authentict
GPL v3