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bamsormadup: add extra test case, fix single file input (#1905)

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Matthias De Smet 2022-07-19 13:52:37 +02:00 committed by GitHub
parent 8002e373b5
commit 6b9a6a5b29
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3 changed files with 25 additions and 5 deletions
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3
modules/biobambam/bamsormadup/main.nf
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@ -22,8 +22,7 @@ process BIOBAMBAM_BAMSORMADUP {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = args.contains("outputformat=cram") ? "cram" : "bam" def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
def input_string = bams.join(" I=") def input_string = bams instanceof List ? bams.join(" I=") : bams
if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output." if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
""" """

12
tests/modules/biobambam/bamsormadup/main.nf
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@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf' include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf'
workflow test_biobambam_bamsormadup { workflow test_biobambam_bamsormadup_multi_input {
input = [ input = [
[ id:'test', single_end:false ], // meta map [ id:'test', single_end:false ], // meta map
@ -13,3 +13,13 @@ workflow test_biobambam_bamsormadup {
BIOBAMBAM_BAMSORMADUP ( input, [] ) BIOBAMBAM_BAMSORMADUP ( input, [] )
} }
workflow test_biobambam_bamsormadup_single_input {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)],
]
BIOBAMBAM_BAMSORMADUP ( input, [] )
}

15
tests/modules/biobambam/bamsormadup/test.yml
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@ -1,5 +1,5 @@
- name: biobambam bamsormadup test_biobambam_bamsormadup - name: biobambam bamsormadup test_biobambam_bamsormadup_multi_input
command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_multi_input -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config
tags: tags:
- biobambam - biobambam
- biobambam/bamsormadup - biobambam/bamsormadup
@ -8,3 +8,14 @@
md5sum: 1d549a00b065584c298594180ca9f3bc md5sum: 1d549a00b065584c298594180ca9f3bc
- path: output/biobambam/test.metrics.txt - path: output/biobambam/test.metrics.txt
md5sum: 1721879bea1f3888ecd33b35e6ee0e72 md5sum: 1721879bea1f3888ecd33b35e6ee0e72
- name: biobambam bamsormadup test_biobambam_bamsormadup_single_input
command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup_single_input -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config
tags:
- biobambam
- biobambam/bamsormadup
files:
- path: output/biobambam/test.bam
md5sum: 48e01431daec7fb17471d930a6d1d587
- path: output/biobambam/test.metrics.txt
md5sum: b97458eff0d4b259055e4902849ee53b