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f7ebc2fc48
* New last/dotplot module for pairwise similarity plots The `last-dotplot` tool takes a pairwise alignment in [MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, possibly compressed with gzip, or in a tabular format produced by the `maf-convert` tool, and produces a similarity dot-plot of the two sequences in one of the graphical formats supported by the Python Imaging Library. A the tool guesses the output format by the file extension of the file, which is constructed by the module at run time, I have used the `args2` option to convey this information to the module. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence please ignore lint's version warning). * Update the functions.nf file to the dev branch. https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
40 lines
1 KiB
YAML
40 lines
1 KiB
YAML
name: last_dotplot
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description: Makes a dotplot (Oxford Grid) of pair-wise sequence alignments
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keywords:
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- LAST
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- plot
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- pair
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- alignment
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- MAF
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tools:
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- last:
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description: LAST finds & aligns related regions of sequences.
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homepage: https://gitlab.com/mcfrith/last
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documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst
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tool_dev_url: https://gitlab.com/mcfrith/last
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doi: ""
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licence: ['GPL-3.0-or-later']
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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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- maf:
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type: file
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description: Multiple Aligment Format (MAF) file, compressed with gzip
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pattern: "*.{maf.gz}"
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output:
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- plot:
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type: file
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description: Pairwise alignment dot plot image, in PNG or other format.
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pattern: "*.{gif,png}"
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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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- "@charles-plessy"
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