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409af2f27c
* feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
42 lines
1.1 KiB
YAML
42 lines
1.1 KiB
YAML
name: gatk4_gatherpileupsummaries
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description: write your description here
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keywords:
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- sort
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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: ["BSD-3-clause"]
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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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- pileup:
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type: (list of) file(s)
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description: Pileup files from gatk4/getpileupsummaries
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pattern: "*.pileups.table"
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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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- table:
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type: file
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description: pileup summaries table file
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pattern: "*.pileupsummaries.table"
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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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authors:
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- "@FriederikeHanssen"
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- "@maxulysse"
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