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080320765c
* 📦 NEW: Add bamtools/convert module * 👌 IMPROVE: Update output channel name, Add tests for each output format * 👌 IMPROVE: Add error test * 🐛 FIX: Remove custom tags Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
104 lines
3.3 KiB
Text
104 lines
3.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf'
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include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf'
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workflow test_bamtools_convert_ext_error {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_EXT_ERROR ( input )
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}
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workflow test_bamtools_convert_noext_error {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
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}
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workflow test_bamtools_convert_bed {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_BED ( input )
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}
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workflow test_bamtools_convert_fasta {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_FASTA ( input )
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}
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workflow test_bamtools_convert_fastq {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_FASTQ ( input )
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}
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workflow test_bamtools_convert_json {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_JSON ( input )
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}
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workflow test_bamtools_convert_pileup {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_PILEUP ( input )
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}
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workflow test_bamtools_convert_sam {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_SAM ( input )
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}
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workflow test_bamtools_convert_yaml {
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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_bam'], checkIfExists: true)
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]
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BAMTOOLS_CONVERT_YAML ( input )
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}
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