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e19a9a2474
* new tool: staden_io_lib * update docker containers * add test.yml * add fai index input * typo * fix version.yml * update md5sum * omit md5sum for cram * move scramble to submodule * add missing in/output * remove some comments Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
58 lines
1.6 KiB
YAML
58 lines
1.6 KiB
YAML
name: "stadeniolib_scramble"
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description: Advanced sequence file format conversions
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keywords:
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- sam
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- bam
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- cram
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- compression
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tools:
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- "scramble":
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description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats."
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homepage: "https://github.com/jkbonfield/io_lib"
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documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
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tool_dev_url: "https://github.com/jkbonfield/io_lib"
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licence: "['BSD']"
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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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- reads:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- fasta:
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type: file
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description: Reference genome in FASTA format
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pattern: "*.{fa,fasta}"
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- fai:
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type: file
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description: FASTA index file from samtools faidx
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pattern: "*.{fai}"
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- gzi:
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type: file
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description: Optional gzip index file for BAM inputs
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pattern: "*.gzi"
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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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- 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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- reads:
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type: file
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description: Converted reads
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pattern: "*.{sam, bam, cram}"
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- gzi:
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type: Optional file
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description: gzip index file for BAM outputs
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pattern: ".{bam.gzi}"
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authors:
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- "@matthdsm"
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