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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>
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: damageprofiler
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description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
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keywords:
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- damage
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- deamination
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- miscoding lesions
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- C to T
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- ancient DNA
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- aDNA
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- palaeogenomics
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- archaeogenomics
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- palaeogenetics
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- archaeogenetics
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tools:
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- damageprofiler:
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description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
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homepage: https://github.com/Integrative-Transcriptomics/DamageProfiler
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documentation: https://damageprofiler.readthedocs.io/
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tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler
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doi: "10.1093/bioinformatics/btab190"
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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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- bam:
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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: OPTIONAL FASTA reference file
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pattern: "*.{fasta,fna,fa}"
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- fai:
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type: file
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description: OPTIONAL FASTA index file from samtools faidx
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pattern: "*.{fai}"
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- specieslist:
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type: file
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description: OPTIONAL text file with list of target reference headers
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pattern: "*.{txt}"
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output:
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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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- results:
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type: dir
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description: DamageProfiler results directory
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pattern: "*/*"
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authors:
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- "@jfy133"
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