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* adding template for module groupreadsbyumi * update modules with code * strategy is required argument so moving it to input rather than options.args * tests successful committing yml * added meta to output Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
59 lines
1.9 KiB
YAML
59 lines
1.9 KiB
YAML
name: fgbio_groupreadsbyumi
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description: |
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Groups reads together that appear to have come from the same original molecule.
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Reads are grouped by template, and then templates are sorted by the 5’ mapping positions
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of the reads from the template, used from earliest mapping position to latest.
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Reads that have the same end positions are then sub-grouped by UMI sequence.
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(!) Note: the MQ tag is required on reads with mapped mates (!)
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This can be added using samblaster with the optional argument --addMateTags.
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keywords:
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- UMI
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- groupreads
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- fgbio
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tools:
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- fgbio:
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description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
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homepage: http://fulcrumgenomics.github.io/fgbio/
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documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
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tool_dev_url: https://github.com/fulcrumgenomics/fgbio
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doi: ""
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licence: ['MIT']
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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: |
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BAM file. Note: the MQ tag is required on reads with mapped mates (!)
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pattern: "*.bam"
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- strategy:
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type: value
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description: |
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Reguired argument: defines the UMI assignment strategy.
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Must be chosen among: Identity, Edit, Adjacency, Paired.
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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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- bam:
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type: file
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description: UMI-grouped BAM
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pattern: "*.bam"
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- histogram:
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type: file
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description: A text file containing the tag family size counts
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pattern: "*.txt"
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authors:
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- "@lescai"
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