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

]

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}

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

Sorted and duplicate marked BAM file

*.bam

cram

meta:map

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

]

*.cram:file

Sorted and duplicate marked CRAM file

*.cram

csi

meta:map

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

]

*.csi:file

Sorted and duplicate marked BAM index file

*.csi

crai

meta:map

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

]

*.crai:file

Sorted and duplicate marked CRAM index file

*.crai

metrics

meta:map

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

]

*.metrics:file

Duplicate metrics file

*.metrics

versions

versions.yml:file

File containing software versions

versions.yml

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

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

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

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

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