nf-core_modules/tests/software/gatk4/mergevcfs/main.nf
suzannejin 989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
workflow test_gatk4_mergevcfs {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
]
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEVCFS ( input, dict, false )
}
workflow test_gatk4_mergevcfs_refdict {
def input = []
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
]
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEVCFS ( input, dict, true )
}