mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
32 lines
1.4 KiB
Text
32 lines
1.4 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
|
||
|
|
include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
|
||
|
|
|
||
|
|
workflow test_samtools_convert_bamtocram {
|
||
|
|
|
||
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
|
||
|
|
SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_samtools_convert_cramtobam {
|
||
|
|
|
||
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
|
||
|
|
SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
|
||
|
|
}
|