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

meta (map)

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

]

bam (file)

Sorted and duplicate marked BAM file

*.bam

cram (file)

Sorted and duplicate marked CRAM file

*.cram

csi (file)

Sorted and duplicate marked BAM index file

*.csi

crai (file)

Sorted and duplicate marked CRAM index file

*.crai

metrics (file)

Duplicate metrics file

*.metrics

versions (file)

File containing software versions

versions.yml
maintainer
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub

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