update tests

tests/modules/cnvpytor/callcnvs/test.yml

@@ -4,7 +4,7 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
@@ -13,5 +13,5 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml

tests/modules/cnvpytor/view/main.nf

@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_VIEW } from '../../../../modules/cnvpytor/view/main.nf'
+
+workflow test_cnvpytor_view {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000 100000"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, [] )
+}
+
+workflow test_cnvpytor_view_tsvout {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000"
+    output_suffix = "tsv"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+}
+
+workflow test_cnvpytor_view_stub {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000"
+    output_suffix = "tsv"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+}

tests/modules/cnvpytor/view/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CNVPYTOR_VIEW {
+        ext.args = '10000 100000'
+    }
+}

tests/modules/cnvpytor/view/test.yml

@@ -0,0 +1,26 @@
+- name: cnvpytor view test_cnvpytor_view
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test_10000.vcf
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view tsv
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view stub
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config  -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test.vcf
+    - path: output/cnvpytor/versions.yml