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a68c563e54
* added code for subworkflow fgbio call umi consensus * ironing out a few typos etc * fixing last things * fixed md5sum - lets see if it changes * removing file accidentally deleted * tidy indents * added bwamem2 alternative * fixed entry for both tests * changed name second test workflow entry * fixed workflow entry names * fixed md5sum for file generated with bwamem2 * added syntax new DSL2 * added new config location in test command line * added new config location in test command line * use of prefix instead of suffix because modules have been changed in this way * explicit alias to bwa mem1 to avoid confusion * removed param that should be an ext optional argument in fgbio groupreadsbyumi * missing colon in config * missing colon in module config too * order list alphabetically Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * remove params from body Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * improving readability of input structure Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * reverting to mandatory input * fixed tests and workflow take values * remove param Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * simplify tests params Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * formatting inputs for readability * factoring in changes to bwamem2_mem and bwa_mem sort/view inputs * updating test md5sum for grouped file following code update in bwamem Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
15 lines
429 B
Text
15 lines
429 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/fgbio/groupreadsbyumi/main.nf'
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workflow test_fgbio_groupreadsbyumi {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_tagged_bam'], checkIfExists: true)
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]
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FGBIO_GROUPREADSBYUMI ( input, 'Adjacency' )
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}
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