added tests

modules/srst2/srst2/main.nf

@@ -11,8 +11,9 @@ process SRST2_SRST2 {
     tuple val(meta), path(fastq_s), path(db)
 
     output:
-    tuple val(meta), path("*_genes_*_results.txt")               ,                emit: gene_results
+    tuple val(meta), path("*_genes_*_results.txt")               , optional:true, emit: gene_results
     tuple val(meta), path("*_fullgenes_*_results.txt")           , optional:true, emit: fullgene_results
+    tuple val(meta), path("*_mlst_*_results.txt")                , optional:true, emit: mlst_results
     tuple val(meta), path("*.pileup")                            ,                emit: pileup
     tuple val(meta), path("*.sorted.bam")                        ,                emit: sorted_bam
     path "versions.yml"                                          ,                emit: versions
@@ -38,7 +39,6 @@ process SRST2_SRST2 {
         --output ${prefix} \\
         ${database} \\
         $args
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))

modules/srst2/srst2/meta.yml

@@ -49,12 +49,16 @@ output:
       pattern: "versions.yml"
   - txt:
       type: file
-      description: A detailed report, with one row per gene per sample described here: https://github.com/katholt/srst2#gene-typing
+      description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
       pattern: "*_fullgenes_*_results.txt"
   - txt:
       type: file
       description: A tabulated summary report of samples x genes.
       pattern: "*_genes_*_results.txt"
+  - txt:
+      type: file
+      description: A tabulated summary report of mlst subtyping.
+      pattern: "*_mlst_*_results.txt"
   - bam:
       type: file
       description: Sorted BAM file

tests/modules/srst2/srst2/main.nf

@@ -4,9 +4,34 @@ nextflow.enable.dsl = 2
 
 include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
 
+workflow test_srst2_srst2_exit {
+
+    input = [
+        [ id:'test', single_end:false, db:"test"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+//        [("")]
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_mlst {
+
+    input = [
+        [ id:'test', single_end:false, db:"mlst"], // meta map
+        [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
+          file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
+    ]
+
+    SRST2_SRST2(input)
+}
+
 workflow test_srst2_srst2_paired_end {
 
-    input = [ 
+    input = [
         [ id:'test', single_end:false, db:"gene"], // meta map
         [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
           file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
@@ -18,11 +43,11 @@ workflow test_srst2_srst2_paired_end {
 
 workflow test_srst2_srst2_single_end {
 
-    input = [ 
+    input = [
         [ id:'test', single_end:true, db:"gene" ], // meta map
         file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
         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
     ]
 
     SRST2_SRST2(input)
-}
+}

tests/modules/srst2/srst2/test.yml

@@ -1,8 +1,22 @@
+- name: srst2 srst2 test_srst2_srst2_mlst
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
+      md5sum: f59217dd9340264b9913c20b545b2ce7
+    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
+    - path: output/srst2/test__mlst__MLST_DB__results.txt
+      md5sum: ec1b1f69933401d67c57f64cad11a098
+    - path: output/srst2/versions.yml
+      md5sum: a0c256a2fd3636069710b8ef22ee5ea7
+
 - name: srst2 srst2 test_srst2_srst2_paired_end
   command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
   tags:
-    - srst2
     - srst2/srst2
+    - srst2
   files:
     - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
       md5sum: 099aa6cacec5524b311f606debdfb3a9
@@ -15,8 +29,8 @@
 - name: srst2 srst2 test_srst2_srst2_single_end
   command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
   tags:
-    - srst2
     - srst2/srst2
+    - srst2
   files:
     - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
       md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
@@ -27,3 +41,6 @@
     - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
     - path: output/srst2/versions.yml
       md5sum: 790fe00493c6634d17801a930073218b
+
+- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
+  exit_code: 1