modules/samtools_stats

Produces comprehensive statistics from SAM/BAM/CRAM file

statisticscountsbamsamcram

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

Description

Produces comprehensive statistics from SAM/BAM/CRAM file

Input

name:type

description

pattern

`meta:map`

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

`input:file`

BAM/CRAM file from alignment

*.{bam,cram}

`input_index:file`

BAI/CRAI file from alignment

*.{bai,crai}

`meta2:map`

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

`fasta:file`

Reference file the CRAM was created with (optional)

*.{fasta,fa}

Output

name:type

description

pattern

`stats`

`meta:map`

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

`*.stats:file`

File containing samtools stats output

*.{stats}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/samtools_stats

Description

Input

meta:map

input:file

input_index:file

meta2:map

fasta:file

Output

stats

meta:map

*.stats:file

versions

versions.yml:file

Tools

samtools MIT

`meta:map`

`input:file`

`input_index:file`

`meta2:map`

`fasta:file`

`stats`

`meta:map`

`*.stats:file`

`versions`

`versions.yml:file`

samtools
MIT