modules/samtools_sormadup

Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file

catcollatefixmatesortmarkduplicatesbamsamcrammulti-tool

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

Description

Collate/Fixmate/Sort/Markdup 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/SAM files

*.{bam,cram,sam}

`meta2`
`:map`

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

`fasta`
`:file`

Reference genome file

*.{fasta,fa,fna}

`fai`
`:file`

Reference genome index file

*.fai

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Sorted and duplicate marked BAM file

*.bam

`cram`

`meta`
`:map`

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

`*.cram`
`:file`

Sorted and duplicate marked CRAM file

*.cram

`csi`

`meta`
`:map`

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

`*.csi`
`:file`

Sorted and duplicate marked BAM index file

*.csi

`crai`

`meta`
`:map`

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

`*.crai`
`:file`

Sorted and duplicate marked CRAM index file

*.crai

`metrics`

`meta`
`:map`

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

`*.metrics`
`:file`

Duplicate metrics file

*.metrics

`versions_samtools`

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

The process the versions were collected from

`samtools`
`:string`

The tool name

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

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`samtools`
`:string`

The tool name

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

The command used to generate the version of the tool

Tools

samtools_cat
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.

args_id: $args

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

samtools_collate
MIT

args_id: $args2

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

samtools_fixmate
MIT

args_id: $args3

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

samtools_sort
MIT

args_id: $args4

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

samtools_markdup
MIT

args_id: $args5

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

modules/samtools_sormadup

Description

Input

meta:map

input:file

meta2:map

fasta:file

fai:file

Output

bam

meta:map

*.bam:file

cram

meta:map

*.cram:file

csi

meta:map

*.csi:file

crai

meta:map

*.crai:file

metrics

meta:map

*.metrics:file

versions_samtools

${task.process}:string

samtools:string

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

Topics

versions

${task.process}:string

samtools:string

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

Tools

samtools_cat MIT

samtools_collate MIT

samtools_fixmate MIT

samtools_sort MIT

samtools_markdup MIT

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`crai`

`meta`
`:map`

`*.crai`
`:file`

`metrics`

`meta`
`:map`

`*.metrics`
`:file`

`versions_samtools`

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

`samtools`
`:string`

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

`versions`

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

`samtools`
`:string`

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

samtools_cat
MIT

samtools_collate
MIT

samtools_fixmate
MIT

samtools_sort
MIT

samtools_markdup
MIT