Description

Collate/Fixmate/Sort/Markdup 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/SAM files

*.{bam,cram,sam}

meta2{:bash}

:map

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

fasta{:bash}

:file

Reference genome file

*.{fasta,fa,fna}

fai{:bash}

:file

Reference genome index file

*.fai

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Sorted and duplicate marked BAM file

*.bam

cram{:bash}

meta{:bash}

:map

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

*.cram{:bash}

:file

Sorted and duplicate marked CRAM file

*.cram

csi{:bash}

meta{:bash}

:map

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

*.csi{:bash}

:file

Sorted and duplicate marked BAM index file

*.csi

crai{:bash}

meta{:bash}

:map

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

*.crai{:bash}

:file

Sorted and duplicate marked CRAM index file

*.crai

metrics{:bash}

meta{:bash}

:map

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

*.metrics{:bash}

:file

Duplicate metrics file

*.metrics

versions_samtools{: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}

:eval

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}

: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

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: $args2
http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

samtools_fixmate
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: $args3
http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

samtools_sort
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: $args4
http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

samtools_markdup
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: $args5
http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
maintainer
Github user matthdsm
get in touch
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