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983ba000c1
* Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
13 lines
666 B
Text
13 lines
666 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FGBIO_SORTBAM } from '../../../../software/fgbio/sortbam/main.nf' addParams( options: [args: '-s TemplateCoordinate', suffix: '_out'] )
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include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../software/fgbio/callmolecularconsensusreads/main.nf' addParams( options: [args: '-M 1', suffix: '_molreads'] )
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workflow test_fgbio_callmolecularconsensusreads {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
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FGBIO_SORTBAM ( input )
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FGBIO_CALLMOLECULARCONSENSUSREADS ( FGBIO_SORTBAM.out.bam )
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}
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