nf-core_modules/modules/samtools/merge/meta.yml

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name: samtools_merge
description: Merge BAM or CRAM file
keywords:
- merge
- bam
- sam
- cram
tools:
- samtools:
description: |
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.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_files:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: optional file
description: Reference file the CRAM was created with
pattern: "*.{fasta,fa}"
2022-07-18 09:37:45 +00:00
- fai:
type: optional file
description: Index of the reference file the CRAM was created with
pattern: "*.fai"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.{bam}"
- cram:
type: file
description: CRAM file
pattern: "*.{cram}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- csi:
type: file
description: BAM index file (optional)
pattern: "*.csi"
authors:
- "@drpatelh"
- "@yuukiiwa "
- "@maxulysse"
- "@FriederikeHanssen"