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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>
56 lines
1.5 KiB
YAML
56 lines
1.5 KiB
YAML
name: gatk4_estimatelibrarycomplexity
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description: Estimates the numbers of unique molecules in a sequencing library.
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keywords:
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- gatk4
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- gatk4_estimatelibrarycomplexity
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- duplication_metrics
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- reporting
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tools:
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- gatk4:
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description: Genome Analysis Toolkit (GATK4)
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us
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tool_dev_url: https://github.com/broadinstitute/gatk
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doi: "10.1158/1538-7445.AM2017-3590"
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licence: ["Apache-2.0"]
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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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- cram:
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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: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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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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- metrics:
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type: file
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description: File containing metrics on the input files
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pattern: "*.{metrics}"
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authors:
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- "@FriederikeHanssen"
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