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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>
59 lines
1.6 KiB
YAML
59 lines
1.6 KiB
YAML
name: tbprofiler_profile
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description: A tool to detect resistance and lineages of M. tuberculosis genomes
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keywords:
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- Mycobacterium tuberculosis
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- resistance
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- serotype
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tools:
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- tbprofiler:
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description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
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homepage: https://github.com/jodyphelan/TBProfiler
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documentation: https://jodyphelan.gitbook.io/tb-profiler/
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tool_dev_url: https://github.com/jodyphelan/TBProfiler
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doi: "10.1186/s13073-019-0650-x"
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licence: ["GPL v3"]
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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: FASTQ file
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pattern: "*.{fastq.gz,fq.gz}"
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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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- bam:
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type: file
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description: BAM file with alignment details
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pattern: "*.bam"
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- csv:
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type: file
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description: Optional CSV formated result file of resistance and strain type
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pattern: "*.csv"
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- json:
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type: file
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description: JSON formated result file of resistance and strain type
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pattern: "*.json"
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- txt:
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type: file
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description: Optional text file of resistance and strain type
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pattern: "*.txt"
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- vcf:
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type: file
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description: VCF with variant info again refernce genomes
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pattern: "*.vcf"
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authors:
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- "@rpetit3"
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