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Updating test file for optitype (#782)

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* Provide an exisiting bam file for optitype

* Update main.nf

Attempt at fixing this with new testing data

* Trying slightly different approach

* Mini fixes, not sure whats wrong here

* Add bam file with NM tags in all reads for optitype

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
This commit is contained in:
Jose Espinosa-Carrasco 2021-10-28 14:24:52 +02:00 committed by GitHub
parent d5183a7fec
commit fd1189c2f5
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 6 additions and 3 deletions
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1
tests/config/test_data.config
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@ -135,6 +135,7 @@ params {
test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"

4
tests/modules/optitype/main.nf
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@ -6,8 +6,8 @@ include { OPTITYPE } from '../../../modules/optitype/main.nf' addParams( options
workflow test_optitype { workflow test_optitype {
input = [ [ id:'test', seq_type:'dna' ], // meta map input = [ [ id:'test', seq_type:'dna' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla'], checkIfExists: true)
] ]
OPTITYPE ( input ) OPTITYPE ( input )
} }

4
tests/modules/optitype/test.yml
View file

@ -3,5 +3,7 @@
tags: tags:
- optitype - optitype
files: files:
- path: output/optitype/test/test_result.tsv
- path: output/optitype/test/test_coverage_plot.pdf - path: output/optitype/test/test_coverage_plot.pdf
- path: output/optitype/test/test_result.tsv
contains:
- '1446'