modules/preseq_ccurve

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

preseqlibrarycomplexity

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

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

`c_curve`

`meta`
`:map`

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

`*.c_curve.txt`
`:file`

Preseq c_curve output file

*.{c_curve.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: //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: //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_ccurve

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`c_curve`

`meta`
`:map`

`*.c_curve.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_preseq`

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

`preseq`
`:string`

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

Topics

`versions`

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

`preseq`
`:string`

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

Tools

preseq
GPL

included in

maintainers

get in touch

modules/preseq_ccurve

Description

Input

meta :map

bam :file

Output

c_curve

meta :map

*.c_curve.txt :file

log

meta :map

*.log :file

versions_preseq

${task.process} :string

preseq :string

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

Topics

versions

${task.process} :string

preseq :string

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

Tools

preseqGPL

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`c_curve`

`meta`
`:map`

`*.c_curve.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_preseq`

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

`preseq`
`:string`

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

`versions`

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

`preseq`
`:string`

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

preseq
GPL