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292e8eceb9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add MALT with incomplete tests * Parameter typo fix * Clean up test yaml * Finish MALT module prior UNZIP and MALT_BUILD modiules * Add required modules for tests * Sync test out with malt-build * Fix input parameters in tests based on final build module * Update modules/malt/run/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: malt_run
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description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
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keywords:
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- malt
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- alignment
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- metagenomics
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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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- microbiome
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tools:
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- malt:
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description: A tool for mapping metagenomic data
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homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
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documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
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tool_dev_url: None
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doi: "10.1038/s41559-017-0446-6"
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licence: ['GPL v3']
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input:
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- fastqs:
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type: file
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description: Input FASTQ files
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pattern: "*.{fastq.gz,fq.gz}"
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- mode:
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type: string
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description: Program mode
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pattern: 'Unknown|BlastN|BlastP|BlastX|Classifier'
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- index:
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type: directory
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description: Index/database directory from malt-build
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pattern: '*/'
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output:
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- rma6:
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type: file
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description: MEGAN6 RMA6 file
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pattern: "*.rma6"
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- sam:
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type: file
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description: Alignment files in Tab, Text or MEGAN-compatible SAM format
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pattern: "*.{tab,txt,sam}"
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- log:
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type: file
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description: Log of verbose MALT stdout
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pattern: "malt-run.log"
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authors:
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- "@jfy133"
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