modules/goleft_indexcov

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that’s what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

coveragecnvgenomicsdepth

https://github.com/nf-core/modules/[...]/modules/nf-core/goleft/indexcov

Description

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that’s what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

Input

name:type

description

pattern

`meta`
`:map`

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

`bams`
`:file`

Sorted BAM/CRAM/SAM files

*.{bam,cram,sam}

`indexes`
`:file`

BAI/CRAI files

*.{bai,crai}

`meta2`
`:map`

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

`fai`
`:file`

FASTA index

*.{fai}

Output

name:type

description

pattern

`output`

`meta`
`:map`

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

`${prefix}/*`
`:file`

Files generated by indexcov

`ped`

`meta`
`:map`

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

`${prefix}/*ped`
`:file`

ped files

*ped

`bed`

`meta`
`:map`

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

`${prefix}/*bed.gz`
`:file`

bed files

*bed.gz

`bed_index`

`meta`
`:map`

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

`${prefix}/*bed.gz.tbi`
`:file`

bed index files

*bed.gz.tbi

`roc`

`meta`
`:map`

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

`${prefix}/*roc`
`:file`

roc files

*roc

`html`

`meta`
`:map`

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

`${prefix}/*html`
`:file`

html files

*html

`png`

`meta`
`:map`

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

`${prefix}/*png`
`:file`

png files

*png

`versions_goleft`

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

The name of the process

`goleft`
`:string`

The name of the tool

`goleft --version |& sed '1!d;s/^.*goleft Version: //'`
`:eval`

The expression to obtain the version of the tool

`versions_tabix`

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

The name of the process

`tabix`
`:string`

The name of the tool

`tabix -h |& 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

`goleft`
`:string`

The name of the tool

`goleft --version |& sed '1!d;s/^.*goleft Version: //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`tabix`
`:string`

The name of the tool

`tabix -h |& sed -n 's/^.*Version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

goleft
MIT

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

github.com/brentp/goleft 10.1093/gigascience/gix090