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added tests
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jvhagey
parent
218769d7df
commit
24dc2d2113
4 changed files with 54 additions and 8 deletions
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@ -11,8 +11,9 @@ process SRST2_SRST2 {
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tuple val(meta), path(fastq_s), path(db)
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output:
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tuple val(meta), path("*_genes_*_results.txt") , emit: gene_results
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tuple val(meta), path("*_genes_*_results.txt") , optional:true, emit: gene_results
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tuple val(meta), path("*_fullgenes_*_results.txt") , optional:true, emit: fullgene_results
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tuple val(meta), path("*_mlst_*_results.txt") , optional:true, emit: mlst_results
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tuple val(meta), path("*.pileup") , emit: pileup
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tuple val(meta), path("*.sorted.bam") , emit: sorted_bam
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path "versions.yml" , emit: versions
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@ -38,7 +39,6 @@ process SRST2_SRST2 {
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--output ${prefix} \\
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${database} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))
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@ -49,12 +49,16 @@ output:
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pattern: "versions.yml"
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- txt:
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type: file
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description: A detailed report, with one row per gene per sample described here: https://github.com/katholt/srst2#gene-typing
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description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
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pattern: "*_fullgenes_*_results.txt"
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- txt:
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type: file
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description: A tabulated summary report of samples x genes.
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pattern: "*_genes_*_results.txt"
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- txt:
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type: file
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description: A tabulated summary report of mlst subtyping.
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pattern: "*_mlst_*_results.txt"
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- bam:
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type: file
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description: Sorted BAM file
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@ -4,9 +4,34 @@ nextflow.enable.dsl = 2
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include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
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workflow test_srst2_srst2_exit {
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input = [
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[ id:'test', single_end:false, db:"test"], // meta map
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[ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
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// [("")]
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
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]
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SRST2_SRST2(input)
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}
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workflow test_srst2_srst2_mlst {
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input = [
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[ id:'test', single_end:false, db:"mlst"], // meta map
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[ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
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file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
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]
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SRST2_SRST2(input)
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}
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workflow test_srst2_srst2_paired_end {
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input = [
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input = [
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[ id:'test', single_end:false, db:"gene"], // meta map
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[ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
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@ -18,11 +43,11 @@ workflow test_srst2_srst2_paired_end {
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workflow test_srst2_srst2_single_end {
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input = [
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input = [
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[ id:'test', single_end:true, db:"gene" ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in tests/config/test_data.config
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]
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SRST2_SRST2(input)
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}
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}
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@ -1,8 +1,22 @@
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- name: srst2 srst2 test_srst2_srst2_mlst
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command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
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tags:
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- srst2/srst2
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- srst2
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files:
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- path: output/srst2/test__SRR9067271.MLST_DB.pileup
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md5sum: f59217dd9340264b9913c20b545b2ce7
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- path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
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- path: output/srst2/test__mlst__MLST_DB__results.txt
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md5sum: ec1b1f69933401d67c57f64cad11a098
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- path: output/srst2/versions.yml
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md5sum: a0c256a2fd3636069710b8ef22ee5ea7
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- name: srst2 srst2 test_srst2_srst2_paired_end
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command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
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tags:
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- srst2
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- srst2/srst2
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- srst2
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files:
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- path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
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md5sum: 099aa6cacec5524b311f606debdfb3a9
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@ -15,8 +29,8 @@
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- name: srst2 srst2 test_srst2_srst2_single_end
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command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
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tags:
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- srst2
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- srst2/srst2
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- srst2
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files:
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- path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
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md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
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@ -27,3 +41,6 @@
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- path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
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- path: output/srst2/versions.yml
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md5sum: 790fe00493c6634d17801a930073218b
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- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
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exit_code: 1
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