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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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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- 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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- 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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