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Merge pull request #1653 from luslab/bowtie2-test-fix

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Bowtie2 test fixes
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Chris Cheshire 2022-05-13 12:32:28 +01:00 committed by GitHub
commit af017b32a5
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4 changed files with 59 additions and 12 deletions
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1
modules/bowtie2/align/main.nf
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@ -69,4 +69,3 @@ process BOWTIE2_ALIGN {
END_VERSIONS END_VERSIONS
""" """
} }

29
tests/modules/bowtie2/align/main.nf
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@ -33,3 +33,32 @@ workflow test_bowtie2_align_paired_end {
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
} }
workflow test_bowtie2_align_single_end_large_index {
input = [
[ id:'test', single_end:true ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
}
workflow test_bowtie2_align_paired_end_large_index {
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 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
}

1
tests/modules/bowtie2/align/nextflow.config
View file

@ -5,6 +5,7 @@ params {
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
} }
if (params.force_large_index) { if (params.force_large_index) {

40
tests/modules/bowtie2/align/test.yml
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@ -1,21 +1,39 @@
- name: bowtie2 align test_bowtie2_align_single_end - name: bowtie2 align test_bowtie2_align_single_end
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags: tags:
- bowtie2/align
- bowtie2 - bowtie2
- bowtie2/align
files: files:
- path: output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
md5sum: 7b8a9e61b7646da1089b041333c41a87 - path: ./output/bowtie2/versions.yml
- path: output/bowtie2/versions.yml
- name: bowtie2 align test_bowtie2_align_paired_end - name: bowtie2 align test_bowtie2_align_paired_end
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config
tags: tags:
- bowtie2/align
- bowtie2 - bowtie2
- bowtie2/align
files: files:
- path: output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
md5sum: bd89ce1b28c93bf822bae391ffcedd19 - path: ./output/bowtie2/versions.yml
- path: output/bowtie2/versions.yml
- name: bowtie2 align test_bowtie2_align_single_end_large_index
command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/versions.yml
- name: bowtie2 align test_bowtie2_align_paired_end_large_index
command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/versions.yml