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43d05d5482
* fix (1852): picard/collectmultiplemetrics supports CRAM Changes: - Add .fai input to Picard CollectMultipleMetrics - Now supports CRAM effectively. - Will break existing pipelines! Fixes #1852 * 1852 Update meta.yml to include .fai
35 lines
1.4 KiB
Text
35 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
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workflow test_picard_collectmultiplemetrics {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, [] )
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}
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workflow test_picard_collectmultiplemetrics_nofasta {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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PICARD_COLLECTMULTIPLEMETRICS ( input, [], [] )
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}
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workflow test_picard_collectmultiplemetrics_cram {
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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_sorted_cram'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
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}
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