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16e8d21477
* add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
21 lines
608 B
Text
21 lines
608 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { NANOPLOT } from '../../../software/nanoplot/main.nf' addParams( options: [:] )
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workflow test_nanoplot_summary {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ] ]
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NANOPLOT ( input )
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}
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workflow test_nanoplot_fastq {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] ]
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NANOPLOT ( input )
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}
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