Restructuring spades tests whith new test data sets + fixing spades tests (#396)

* Restructuring with new test data sets + fixing tests

* Remove checkings for warning files

* Remove md5 check for test.gene_clusters.fa

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

tests/software/spades/main.nf

@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
+
+workflow test_spades_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    coronaspades = false
+
+    SPADES ( input, [], coronaspades )
+}
+
+workflow test_spades_paired_end {
+    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) ]
+            ]
+    coronaspades = false
+
+    SPADES ( input, [], coronaspades )
+}
+
+workflow test_coronospades_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    coronaspades = true
+
+    SPADES ( input, [], coronaspades )
+}
+
+workflow test_coronospades_paired_end {
+    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) ]
+            ]
+    coronaspades = true
+
+    SPADES ( input, [], coronaspades )
+}
+

tests/software/spades/test.yml

@@ -5,13 +5,12 @@
     - spades_single_end
   files:
     - path: output/spades/test.assembly.gfa
-      md5sum: f15ad4a198324de37c6010dafb3fe781
+      md5sum: b2616d2beba83ab7d361b54778d1e759
     - path: output/spades/test.contigs.fa
-      md5sum: bc21771042b465c26dfc85beedc33d58
+      md5sum: 2690fefde046bc904e90df09a065257a
     - path: output/spades/test.scaffolds.fa
-      md5sum: bc21771042b465c26dfc85beedc33d58
+      md5sum: 2690fefde046bc904e90df09a065257a
     - path: output/spades/test.spades.log
-    - path: output/spades/warnings.log
 
 - name: spades paired end
   command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
@@ -20,13 +19,10 @@
     - spades_paired_end
   files:
       - path: output/spades/test.assembly.gfa
-        md5sum: 5da5b04c6fce549c77a209034a9c1e72
+        md5sum: d546f9042f5ff911757e895e7b21f620
       - path: output/spades/test.contigs.fa
-        md5sum: 403b612d52edf390f662ab601873f09f
-      - path: output/spades/test.scaffolds.fa
-        md5sum: 49a9cbb29cee4d088e05e62eb4bc77c4
+        md5sum: f3e87d68521aa485d70aecd82de519b4
       - path: output/spades/test.spades.log
-      - path: output/spades/warnings.log
 
 - name: coronaspades single end
   command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
@@ -40,19 +36,19 @@
         md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
       - path: output/spades/test.scaffolds.fa
         md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
+      - path: output/spades/test.gene_clusters.fa
       - path: output/spades/test.spades.log
 
 - name: coronaspades paired end
-  command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/spades -entry test_coronospades_paired_end -c tests/config/nextflow.config
   tags:
     - spades
     - coronaspades_paired_end
   files:
       - path: output/spades/test.assembly.gfa
-        md5sum: 46531ec9b845c1a1cb469627688fecb7
+        md5sum: d546f9042f5ff911757e895e7b21f620
       - path: output/spades/test.contigs.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.scaffolds.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
+        md5sum: f3e87d68521aa485d70aecd82de519b4
+      - path: output/spades/test.gene_clusters.fa
       - path: output/spades/test.spades.log