modules/mosdepth

Calculates genome-wide sequencing coverage.

mosdepthbamcramcoverage

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

Description

Calculates genome-wide sequencing coverage.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Input BAM/CRAM file

*.{bam,cram}

`bai`
`:file`

Index for BAM/CRAM file

*.{bai,crai}

`bed`
`:file`

BED file with intersected intervals

*.{bed}

`meta2`
`:map`

Groovy Map containing bed information e.g. [ id:‘test’ ]

`fasta`
`:file`

Reference genome FASTA file

*.{fa,fasta}

`quantize_labels`
`:list`

List of labels for quantized coverage bins, e.g. [ “NO_COVERAGE”, “LOW_COVERAGE”, “MEDIUM_COVERAGE”, “HIGH_COVERAGE” ] The first value will be assigned to the MOSDEPTH_Q0 environment variable, the second to MOSDEPTH_Q1, and so on. These can then be used in the --quantize option of mosdepth to assign labels to quantized coverage bins.

Output

name:type

description

pattern

`global_txt`

`meta`
`:map`

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

`*.global.dist.txt`
`:file`

Text file with global cumulative coverage distribution

*.{global.dist.txt}

`summary_txt`

`meta`
`:map`

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

`*.summary.txt`
`:file`

Text file with summary mean depths per chromosome and regions

*.{summary.txt}

`regions_txt`

`meta`
`:map`

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

`*.region.dist.txt`
`:file`

Text file with region cumulative coverage distribution

*.{region.dist.txt}

`per_base_d4`

`meta`
`:map`

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

`*.per-base.d4`
`:file`

D4 file with per-base coverage

*.{per-base.d4}

`per_base_bed`

`meta`
`:map`

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

`*.per-base.bed.gz`
`:file`

BED file with per-base coverage

*.{per-base.bed.gz}

`per_base_csi`

`meta`
`:map`

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

`*.per-base.bed.gz.csi`
`:file`

Index file for BED file with per-base coverage

*.{per-base.bed.gz.csi}

`regions_bed`

`meta`
`:map`

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

`*.regions.bed.gz`
`:file`

BED file with per-region coverage

*.{regions.bed.gz}

`regions_csi`

`meta`
`:map`

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

`*.regions.bed.gz.csi`
`:file`

Index file for BED file with per-region coverage

*.{regions.bed.gz.csi}

`quantized_bed`

`meta`
`:map`

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

`*.quantized.bed.gz`
`:file`

BED file with binned coverage

*.{quantized.bed.gz}

`quantized_csi`

`meta`
`:map`

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

`*.quantized.bed.gz.csi`
`:file`

Index file for BED file with binned coverage

*.{quantized.bed.gz.csi}

`thresholds_bed`

`meta`
`:map`

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

`*.thresholds.bed.gz`
`:file`

BED file with the number of bases in each region that are covered at or above each threshold

*.{thresholds.bed.gz}

`thresholds_csi`

`meta`
`:map`

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

`*.thresholds.bed.gz.csi`
`:file`

Index file for BED file with threshold coverage

*.{thresholds.bed.gz.csi}

`versions_mosdepth`

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

The process the versions were collected from

`mosdepth`
`:string`

The tool name

`mosdepth --version | sed 's/mosdepth //g'`
`:eval`

The command used to generate the version of the tool

`versions_gzip`

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

The process the versions were collected from

`gzip`
`:string`

The name of the tool

`gzip -V 2>&1 | sed 's/gzip $[0-9.]$./\1/;q'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`mosdepth`
`:string`

The tool name

`mosdepth --version | sed 's/mosdepth //g'`
`:eval`

The command used to generate the version of the tool

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

The process the versions were collected from

`gzip`
`:string`

The name of the tool

`gzip -V 2>&1 | sed 's/gzip $[0-9.]$./\1/;q'`
`:eval`

The expression to obtain the version of the tool

Tools

mosdepth
MIT

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

github.com/brentp/mosdepth 10.1093/bioinformatics/btx699

modules/mosdepth

Description

Input

meta:map

bam:file

bai:file

bed:file

meta2:map

fasta:file

quantize_labels:list

Output

global_txt

meta:map

*.global.dist.txt:file

summary_txt

meta:map

*.summary.txt:file

regions_txt

meta:map

*.region.dist.txt:file

per_base_d4

meta:map

*.per-base.d4:file

per_base_bed

meta:map

*.per-base.bed.gz:file

per_base_csi

meta:map

*.per-base.bed.gz.csi:file

regions_bed

meta:map

*.regions.bed.gz:file

regions_csi

meta:map

*.regions.bed.gz.csi:file

quantized_bed

meta:map

*.quantized.bed.gz:file

quantized_csi

meta:map

*.quantized.bed.gz.csi:file

thresholds_bed

meta:map

*.thresholds.bed.gz:file

thresholds_csi

meta:map

*.thresholds.bed.gz.csi:file

versions_mosdepth

${task.process}:string

mosdepth:string

mosdepth --version | sed 's/mosdepth //g':eval

versions_gzip

${task.process}:string

gzip:string

gzip -V 2>&1 | sed 's/gzip \([0-9.]*\).*/\1/;q':eval

Topics

versions

${task.process}:string

mosdepth:string

mosdepth --version | sed 's/mosdepth //g':eval

${task.process}:string

gzip:string

gzip -V 2>&1 | sed 's/gzip \([0-9.]*\).*/\1/;q':eval

Tools

mosdepth MIT

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`quantize_labels`
`:list`

`global_txt`

`meta`
`:map`

`*.global.dist.txt`
`:file`

`summary_txt`

`meta`
`:map`

`*.summary.txt`
`:file`

`regions_txt`

`meta`
`:map`

`*.region.dist.txt`
`:file`

`per_base_d4`

`meta`
`:map`

`*.per-base.d4`
`:file`

`per_base_bed`

`meta`
`:map`

`*.per-base.bed.gz`
`:file`

`per_base_csi`

`meta`
`:map`

`*.per-base.bed.gz.csi`
`:file`

`regions_bed`

`meta`
`:map`

`*.regions.bed.gz`
`:file`

`regions_csi`

`meta`
`:map`

`*.regions.bed.gz.csi`
`:file`

`quantized_bed`

`meta`
`:map`

`*.quantized.bed.gz`
`:file`

`quantized_csi`

`meta`
`:map`

`*.quantized.bed.gz.csi`
`:file`

`thresholds_bed`

`meta`
`:map`

`*.thresholds.bed.gz`
`:file`

`thresholds_csi`

`meta`
`:map`

`*.thresholds.bed.gz.csi`
`:file`

`versions_mosdepth`

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

`mosdepth`
`:string`

`mosdepth --version | sed 's/mosdepth //g'`
`:eval`

`versions_gzip`

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

`gzip`
`:string`

`gzip -V 2>&1 | sed 's/gzip \([0-9.]\)./\1/;q'`
`:eval`

`versions`

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

`mosdepth`
`:string`

`mosdepth --version | sed 's/mosdepth //g'`
`:eval`

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

`gzip`
`:string`

`gzip -V 2>&1 | sed 's/gzip \([0-9.]\)./\1/;q'`
`:eval`

mosdepth
MIT