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f57f085912
* add snapaligner/index * output fixes * fix outputs * fix tests * update inputs * fix more bugs * fix linting * Update modules/snapaligner/index/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/snapaligner/index/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix comments * fix indents * fix escaping Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
39 lines
1.3 KiB
YAML
39 lines
1.3 KiB
YAML
name: "snapaligner_index"
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description: Create a SNAP index for reference genome
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keywords:
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- index
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- fasta
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- genome
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- reference
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tools:
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- "snapaligner":
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description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
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homepage: "http://snap.cs.berkeley.edu"
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documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
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tool_dev_url: "https://github.com/amplab/snap"
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doi: "10.1101/2021.11.23.469039"
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licence: "['Apache v2']"
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input:
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- fasta:
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type: file
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description: Input genome fasta file
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- altcontigfile:
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type: file
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description: Optional file with a list of alt contig names, one per line.
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- nonaltcontigfile:
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type: file
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description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
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- altliftoverfile:
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type: file
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description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
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output:
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- index:
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type: file
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description: SNAP genome index files
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pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
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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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authors:
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- "@matthdsm"
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