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{:bash}

:map

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

bams{:bash}

:file

Sorted BAM/CRAM/SAM files

*.{bam,cram,sam}

indexes{:bash}

:file

BAI/CRAI files

*.{bai,crai}

meta2{:bash}

:map

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

fai{:bash}

:file

FASTA index

*.{fai}

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

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

${prefix}/*{:bash}

:file

Files generated by indexcov

ped{:bash}

meta{:bash}

:map

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

${prefix}/*ped{:bash}

:file

ped files

*ped

bed{:bash}

meta{:bash}

:map

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

${prefix}/*bed.gz{:bash}

:file

bed files

*bed.gz

bed_index{:bash}

meta{:bash}

:map

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

${prefix}/*bed.gz.tbi{:bash}

:file

bed index files

*bed.gz.tbi

roc{:bash}

meta{:bash}

:map

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

${prefix}/*roc{:bash}

:file

roc files

*roc

html{:bash}

meta{:bash}

:map

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

${prefix}/*html{:bash}

:file

html files

*html

png{:bash}

meta{:bash}

:map

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

${prefix}/*png{:bash}

:file

png files

*png

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
sarek
maintainer
Github user lindenb
get in touch
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