DRAFT: Extend output from snpeff (#1895)

* Extending output from snpEff

* Test of additional output-files from snpEff

* Removing some md5 checks

modules/snpeff/main.nf

@@ -15,6 +15,8 @@ process SNPEFF {
     output:
     tuple val(meta), path("*.ann.vcf"), emit: vcf
     path "*.csv"                      , emit: report
+    path "*.html"                     , emit: summary_html
+    path "*.genes.txt"                , emit: genes_txt
     path "versions.yml"               , emit: versions
 
     when:

modules/snpeff/meta.yml

@@ -36,8 +36,16 @@ output:
       pattern: "*.ann.vcf"
   - report:
       type: file
-      description: snpEff report file
+      description: snpEff report csv file
+      pattern: "*.csv"
+  - summary_html:
+      type: file
+      description: snpEff summary statistics in html file
       pattern: "*.html"
+  - genes_txt:
+      type: file
+      description: txt (tab separated) file having counts of the number of variants affecting each transcript and gene
+      pattern: "*.genes.txt"
   - versions:
       type: file
       description: File containing software versions

tests/modules/snpeff/test.yml

@@ -6,3 +6,6 @@
     - path: output/snpeff/test.ann.vcf
       md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
     - path: output/snpeff/test.csv
+    - path: output/snpeff/test.genes.txt
+      md5sum: 130536bf0237d7f3f746d32aaa32840a
+    - path: output/snpeff/snpEff_summary.html