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Update delly/call version (#1991)

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updated version + added tests
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nvnieuwk 2022-09-02 10:08:41 +02:00 committed by GitHub
parent 01d6d4c286
commit 49825425bb
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3 changed files with 31 additions and 7 deletions
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6
modules/delly/call/main.nf
View file

@ -2,10 +2,10 @@ process DELLY_CALL {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::delly=0.8.7" : null) conda (params.enable_conda ? "bioconda::delly=1.1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/delly:0.8.7--he03298f_1' : 'https://depot.galaxyproject.org/singularity/delly:1.1.3--h358d541_0' :
'quay.io/biocontainers/delly:0.8.7--he03298f_1' }" 'quay.io/biocontainers/delly:1.1.3--h358d541_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai)

14
tests/modules/delly/call/main.nf
View file

@ -4,12 +4,24 @@ nextflow.enable.dsl = 2
include { DELLY_CALL } from '../../../../modules/delly/call/main.nf' include { DELLY_CALL } from '../../../../modules/delly/call/main.nf'
workflow test_delly_call { workflow test_delly_call_bam {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], 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)
DELLY_CALL ( input, fasta, fai )
}
workflow test_delly_call_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),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)

18
tests/modules/delly/call/test.yml
View file

@ -1,9 +1,21 @@
- name: delly call test_delly_call - name: delly call test_delly_call_bam
command: nextflow run ./tests/modules/delly/call -entry test_delly_call -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config command: nextflow run ./tests/modules/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
tags: tags:
- delly
- delly/call - delly/call
- delly
files: files:
- path: output/delly/test.bcf - path: output/delly/test.bcf
md5sum: 9d036b140c1bdeab08b7ee6781940fb4
- path: output/delly/test.bcf.csi
md5sum: c198abfc14584c5ac69c004057927e0b
- name: delly call test_delly_call_cram
command: nextflow run ./tests/modules/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
tags:
- delly/call
- delly
files:
- path: output/delly/test.bcf
md5sum: 6c1ec4cfb05ffe9fd93316d2209608ae
- path: output/delly/test.bcf.csi - path: output/delly/test.bcf.csi
md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271 md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271