modules/deeptools_bamcoverage

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

coveragedepthtrack

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

Description

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file

*.{bam,cram}

`input_index`
`:file`

BAM/CRAM index file

*.{bai,crai}

`fasta`
`:file`

Reference file the CRAM file was created with (required with CRAM input)

*.{fasta,fa}

`fasta_fai`
`:file`

Index of the reference file (optional, but recommended)

*.{fai}

`meta2`
`:map`

Groovy Map containing blacklist metadata e.g. [ id:‘blacklist’ ]

`blacklist`
`:file`

BED/GTF file containing regions to exclude from analysis

*.{bed,gtf}

Output

name:type

description

pattern

`bigwig`

`meta`
`:map`

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

`*.bigWig`
`:file`

BigWig file

*.bigWig

`bedgraph`

`meta`
`:map`

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

`*.bedgraph`
`:file`

Bedgraph file

*.bedgraph

`versions_deeptools`

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

The name of the process

`deeptools`
`:string`

The name of the tool

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`deeptools`
`:string`

The name of the tool

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

deeptools
GPL v3

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools.readthedocs.io/en/develop/content/tools/bamCoverage https://github.com/deeptools/deepTools/ 10.1093/nar/gkw257

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

modules/deeptools_bamcoverage

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`meta2`
`:map`

`blacklist`
`:file`

Output

`bigwig`

`meta`
`:map`

`*.bigWig`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedgraph`
`:file`

`versions_deeptools`

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

`deeptools`
`:string`

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Topics

`versions`

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

`deeptools`
`:string`

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Tools

deeptools
GPL v3

samtools
MIT

included in

maintainers

get in touch

modules/deeptools_bamcoverage

Description

Input

meta :map

input :file

input_index :file

fasta :file

fasta_fai :file

meta2 :map

blacklist :file

Output

bigwig

meta :map

*.bigWig :file

bedgraph

meta :map

*.bedgraph :file

versions_deeptools

${task.process} :string

deeptools :string

bamCoverage --version | sed "s/bamCoverage //g" :eval

versions_samtools

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Topics

versions

${task.process} :string

deeptools :string

bamCoverage --version | sed "s/bamCoverage //g" :eval

${task.process} :string

samtools :string

samtools version | sed '1!d;s/.* //' :eval

Tools

deeptoolsGPL v3

samtoolsMIT

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`meta2`
`:map`

`blacklist`
`:file`

`bigwig`

`meta`
`:map`

`*.bigWig`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedgraph`
`:file`

`versions_deeptools`

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

`deeptools`
`:string`

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`deeptools`
`:string`

`bamCoverage --version | sed "s/bamCoverage //g"`
`:eval`

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

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

deeptools
GPL v3

samtools
MIT