mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 23:43:19 -05:00
979e57b7ac
* update tests * update * update * make the manta inputs consistant for germline/somatic/tumoronly * match chromosomes to cram file (chr21) * undo genotypegvfs * undo genotypegvfs * update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai) * update tests * fix typos * fix typos Co-authored-by: Smith Nicholas <smith@in.tum.de>
40 lines
2.1 KiB
Text
40 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf'
|
|
|
|
workflow test_manta_somatic {
|
|
|
|
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),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
|
[], []
|
|
]
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
|
|
|
MANTA_SOMATIC ( input, fasta, fai )
|
|
}
|
|
|
|
workflow test_manta_somatic_target_bed {
|
|
|
|
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),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
|
|
]
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
|
|
|
MANTA_SOMATIC ( input, fasta, fai )
|
|
}
|