Description

Produces comprehensive statistics from SAM/BAM/CRAM file

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index{:bash}

:file

BAI/CRAI file from alignment

*.{bai,crai}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta{:bash}

:file

Reference file the CRAM was created with (optional)

*.{fasta,fa}

Output

name:type
description
pattern

stats{:bash}

meta{:bash}

:map

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

*.stats{:bash}

:file

File containing samtools stats output

*.{stats}

versions_samtools{:bash}

${task.process}{:bash}

:string

Name of the process

samtools{:bash}

:string

Name of the tool

samtools version | sed "1!d;s/.* //{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed "1!d;s/.* //{:bash}

:string

The command used to generate the version of the tool

Tools

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
included in
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maintainers
Github user drpatelh
Github user FriederikeHanssen
Github user ramprasadn
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