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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
23 lines
707 B
Text
23 lines
707 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LAST_DOTPLOT } from '../../../../software/last/dotplot/main.nf' addParams( options: [:] )
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workflow test_last_dotplot {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
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LAST_DOTPLOT ( input )
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}
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include { LAST_DOTPLOT as LAST_DOTPLOT_GIF } from '../../../../software/last/dotplot/main.nf' addParams( options: [args2:'gif'] )
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workflow test_last_dotplot_gif {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
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LAST_DOTPLOT_GIF ( input )
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}
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