mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
46 lines
2.7 KiB
Text
46 lines
2.7 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_gatk4_applybqsr {
|
|
input = [ [ id:'test' ], // 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),
|
|
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], 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)
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
|
|
|
GATK4_APPLYBQSR ( input, fasta, fai, dict, [] )
|
|
}
|
|
|
|
workflow test_gatk4_applybqsr_intervals {
|
|
input = [ [ id:'test' ], // 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),
|
|
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], 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)
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
|
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
|
|
|
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
|
|
}
|
|
|
|
workflow test_gatk4_applybqsr_cram {
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], 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)
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
|
intervals = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
|
|
|
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
|
|
}
|