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`

`versions.yml:file`

File containing software versions

versions.yml

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`

`versions.yml:file`

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

versions.yml:file

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`

`versions.yml:file`

authentict
GPL v3