mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { FGBIO_SORTBAM } from '../../../../software/fgbio/sortbam/main.nf' addParams( options: [args: '-s TemplateCoordinate', suffix: '_out'] )
|
|
include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../software/fgbio/callmolecularconsensusreads/main.nf' addParams( options: [args: '-M 1', suffix: '_molreads'] )
|
|
|
|
workflow test_fgbio_callmolecularconsensusreads {
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
|
|
FGBIO_SORTBAM ( input )
|
|
FGBIO_CALLMOLECULARCONSENSUSREADS ( FGBIO_SORTBAM.out.bam )
|
|
}
|