mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf'
|
|
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf'
|
|
|
|
workflow test_bamtools_convert_ext_error {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_EXT_ERROR ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_noext_error {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_bed {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_BED ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_fasta {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_FASTA ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_fastq {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_FASTQ ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_json {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_JSON ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_pileup {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_PILEUP ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_sam {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_SAM ( input )
|
|
}
|
|
|
|
workflow test_bamtools_convert_yaml {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
BAMTOOLS_CONVERT_YAML ( input )
|
|
}
|
|
|