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Update stubs for bwa mem #3671

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merged 1 commit into from
Jul 26, 2023
Merged

Update stubs for bwa mem #3671

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12 changes: 12 additions & 0 deletions modules/nf-core/bwa/mem/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -40,4 +40,16 @@ process BWA_MEM {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
41 changes: 41 additions & 0 deletions tests/modules/nf-core/bwa/mem/main.nf
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Expand Up @@ -82,3 +82,44 @@ workflow test_bwa_mem_paired_end_sort {
BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index, true )
}


//
// Test with stub pairedend
//
workflow test_bwa_mem_paired_end_stub {
input = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
fasta = [
[id: 'test'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]

BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index, false )
}


//
// Test with single-end data stub
//
workflow test_bwa_mem_single_end_stub {
input = [
[ id:'test', single_end:true ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
]
fasta = [
[id: 'test'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]

BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index, false )
}
16 changes: 16 additions & 0 deletions tests/modules/nf-core/bwa/mem/test.yml
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Expand Up @@ -69,3 +69,19 @@
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1

- name: bwa mem paired-end stub
command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config -stub
tags:
- bwa
- bwa/mem
files:
- path: ./output/bwa/test.bam

- name: bwa mem single-end stub
command: nextflow run ./tests/modules/nf-core/bwa/mem -entry test_bwa_mem_single_end_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bwa/mem/nextflow.config -stub
tags:
- bwa
- bwa/mem
files:
- path: ./output/bwa/test.bam
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