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* [samtools] add optional csi output, when applicable * Remove empty line Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
62 lines
1.6 KiB
YAML
62 lines
1.6 KiB
YAML
name: samtools_merge
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description: Merge BAM or CRAM file
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keywords:
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- merge
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- bam
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- sam
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- cram
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input_files:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram,sam}"
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- fasta:
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type: optional file
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description: Reference file the CRAM was created with
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pattern: "*.{fasta,fa}"
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- fai:
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type: optional file
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description: Index of the reference file the CRAM was created with
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pattern: "*.fai"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: CRAM file
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pattern: "*.{cram}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- csi:
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type: file
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description: BAM index file (optional)
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pattern: "*.csi"
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authors:
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- "@drpatelh"
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- "@yuukiiwa "
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- "@maxulysse"
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- "@FriederikeHanssen"
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