mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
12afb6b0fa
* feat added index as input, to allow module to be used for subsampling * fix test * feat added index to meta.yml * Update modules/samtools/view/meta.yml feat corrected description of idea pattern file in meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
24 lines
890 B
Text
24 lines
890 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
|
|
|
|
workflow test_samtools_view {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
|
|
[]
|
|
]
|
|
|
|
SAMTOOLS_VIEW ( input, [] )
|
|
}
|
|
|
|
workflow test_samtools_view_cram {
|
|
input = [ [ id: 'test' ], // 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)
|
|
|
|
SAMTOOLS_VIEW ( input, fasta )
|
|
}
|