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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
46 lines
1.1 KiB
YAML
46 lines
1.1 KiB
YAML
name: lofreq_call
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description: Lofreq subcommand to call low frequency variants from alignments
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keywords:
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- variant calling
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- low frequency variant calling
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- lofreq
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- lofreq/call
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tools:
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- lofreq:
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description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
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homepage: https://csb5.github.io/lofreq/
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documentation: https://csb5.github.io/lofreq/commands/
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doi: "10.1093/nar/gks918 "
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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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- bam:
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type: file
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description: BAM input file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: The reference fasta file
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- vcf:
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type: file
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description: VCF output file
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pattern: "*.{vcf}"
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authors:
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- "@bjohnnyd"
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