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Added extra tests but error with collection

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This commit is contained in:
Chris Cheshire 2022-05-12 10:01:33 +01:00
parent 4bb0423a1d
commit 90c67794bf
4 changed files with 71 additions and 16 deletions
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1
modules/bowtie2/align/main.nf
View file

@ -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) {

56
tests/modules/bowtie2/align/test.yml
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@ -1,21 +1,47 @@
- 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 # md5sum: 7b8a9e61b7646da1089b041333c41a87
- path: output/bowtie2/versions.yml # - path: output/bowtie2/versions.yml
# md5sum: 24621c58884fe90c2255ccd1fe4352ae
- 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 # md5sum: bd89ce1b28c93bf822bae391ffcedd19
- path: output/bowtie2/versions.yml # - path: output/bowtie2/versions.yml
# md5sum: f9712ca6d75393ad5c1781a2dcf82d32
# - 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
# md5sum: 7b8a9e61b7646da1089b041333c41a87
# - path: output/bowtie2/versions.yml
# md5sum: bf0537964a85ce9461ae1b0e2f260211
# - 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
# md5sum: bd89ce1b28c93bf822bae391ffcedd19
# - path: output/bowtie2/versions.yml
# md5sum: c0a88953500eaf46de7ff378a7de4a37