mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
Merge pull request #1653 from luslab/bowtie2-test-fix
Bowtie2 test fixes
This commit is contained in:
commit
af017b32a5
4 changed files with 59 additions and 12 deletions
|
@ -69,4 +69,3 @@ process BOWTIE2_ALIGN {
|
||||||
END_VERSIONS
|
END_VERSIONS
|
||||||
"""
|
"""
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -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 )
|
||||||
|
}
|
|
@ -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) {
|
||||||
|
|
|
@ -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
|
||||||
|
|
Loading…
Reference in a new issue