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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: salmon_quant
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description: gene/transcript quantification with Salmon
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keywords:
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- index
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- fasta
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- genome
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- reference
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tools:
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- salmon:
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description: |
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Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
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homepage: https://salmon.readthedocs.io/en/latest/salmon.html
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manual: https://salmon.readthedocs.io/en/latest/salmon.html
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doi: 10.1038/nmeth.4197
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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: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: directory
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description: Folder containing the star index files
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- gtf:
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type: file
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description: GTF of the reference transcriptome
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- transcriptome_fasta:
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type: file
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description: Fasta file of the reference transcriptome
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- alignment_mode:
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type: boolean
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description: whether to run salmon in alignment mode
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- lib_type:
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type: string
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description: |
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Override library type inferred based on strandedness defined in meta object
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output:
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- sample_output:
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type: directory
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description: Folder containing the quantification results for a specific sample
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pattern: "${prefix}"
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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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authors:
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- "@kevinmenden"
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- "@drpatelh"
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