modules/preseq_lcextrap

Software for predicting library complexity and genome coverage in high-throughput sequencing

preseqlibrarycomplexity

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

Description

Software for predicting library complexity and genome coverage in high-throughput sequencing

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

*.{bam,cram,sam}

Output

name:type

description

pattern

`lc_extrap`

`meta`
`:map`

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

`*.lc_extrap.txt`
`:file`

File containing output of Preseq lcextrap

*.{lc_extrap.txt}

`log`

`meta`
`:map`

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

`*.log`
`:file`

Log file containing stderr produced by Preseq

*.{log}

`versions_preseq`

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

The name of the process

`preseq`
`:string`

The name of the tool

`preseq 2>&1 | sed -n 's/.Version: $.$/\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`preseq`
`:string`

The name of the tool

`preseq 2>&1 | sed -n 's/.Version: $.$/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

preseq
GPL

Software for predicting library complexity and genome coverage in high-throughput sequencing

http://smithlabresearch.org/software/preseq http://smithlabresearch.org/wp-content/uploads/manual.pdf https://github.com/smithlabcode/preseq

modules/preseq_lcextrap

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`lc_extrap`

`meta`
`:map`

`*.lc_extrap.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_preseq`

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

`preseq`
`:string`

`preseq 2>&1 | sed -n 's/.Version: \(.\)/\1/p'`
`:eval`

Topics

`versions`

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

`preseq`
`:string`

`preseq 2>&1 | sed -n 's/.Version: \(.\)/\1/p'`
`:eval`

Tools

preseq
GPL

included in

maintainers

get in touch

modules/preseq_lcextrap

Description

Input

meta:map

bam:file

Output

lc_extrap

meta:map

*.lc_extrap.txt:file

log

meta:map

*.log:file

versions_preseq

${task.process}:string

preseq:string

preseq 2>&1 | sed -n 's/.*Version: \(.*\)/\1/p':eval

Topics

versions

${task.process}:string

preseq:string

preseq 2>&1 | sed -n 's/.*Version: \(.*\)/\1/p':eval

Tools

preseq GPL

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`lc_extrap`

`meta`
`:map`

`*.lc_extrap.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_preseq`

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

`preseq`
`:string`

`preseq 2>&1 | sed -n 's/.Version: \(.\)/\1/p'`
`:eval`

`versions`

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

`preseq`
`:string`

`preseq 2>&1 | sed -n 's/.Version: \(.\)/\1/p'`
`:eval`

preseq
GPL