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Add BAM indexes as input for optitype module. (#1388)

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Michael L Heuer 2022-03-15 11:02:40 -05:00 committed by GitHub
parent 18e72fa0be
commit 73aaecbc3a
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5 changed files with 10 additions and 4 deletions
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2
modules/optitype/main.nf
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@ -8,7 +8,7 @@ process OPTITYPE {
'quay.io/biocontainers/optitype:1.3.5--0' }" 'quay.io/biocontainers/optitype:1.3.5--0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(bai)
output: output:
tuple val(meta), path("${prefix}"), emit: output tuple val(meta), path("${prefix}"), emit: output

4
modules/optitype/meta.yml
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@ -22,6 +22,10 @@ input:
type: file type: file
description: BAM file description: BAM file
pattern: "*.{bam}" pattern: "*.{bam}"
- bai:
type: file
description: BAM index file
pattern: "*.{bai}"
output: output:
- meta: - meta:

3
tests/config/test_data.config
View file

@ -192,7 +192,8 @@ params {
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
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"
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"

3
tests/modules/optitype/main.nf
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@ -6,7 +6,8 @@ include { OPTITYPE } from '../../../modules/optitype/main.nf'
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_hla'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam_bai'], checkIfExists: true)
] ]
OPTITYPE ( input ) OPTITYPE ( input )

2
tests/modules/optitype/test.yml
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@ -6,4 +6,4 @@
- path: output/optitype/test/test_coverage_plot.pdf - path: output/optitype/test/test_coverage_plot.pdf
- path: output/optitype/test/test_result.tsv - path: output/optitype/test/test_result.tsv
contains: contains:
- "1446" - "1439"