mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
7fdeed5b79
* added template
* integrated module
* added fasta index info
* test works, have placeholder data for baits until test-data PR is merged
* added new files to config
* updated test files
* fixing fails ✨
* okay final fix here on the md5sum :face_palm:
* md5sum variable
* update meta.yml to reflect consistency to main.nf
* reverted version so conda works
* Apply suggestions from code review
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* md5sum can't be generated consistently for output
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
18 lines
881 B
Text
18 lines
881 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf' addParams( options: [:] )
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workflow test_picard_collecthsmetrics {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
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}
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