gappa/examineassign: Explicitly output two optional files (#2086)

* gappa/examineassign: Explicitly output two optional files

* Check versions.yml for md5 sum instead

modules/gappa/examineassign/main.nf

@@ -16,6 +16,8 @@ process GAPPA_EXAMINEASSIGN {
     tuple val(meta), path("*profile.tsv")         , emit: profile
     tuple val(meta), path("*labelled_tree.newick"), emit: labelled_tree
     tuple val(meta), path("*per_query.tsv")       , emit: per_query, optional: true
+    tuple val(meta), path("*krona.profile")       , emit: krona    , optional: true
+    tuple val(meta), path("*sativa.tsv")          , emit: sativa   , optional: true
     path "versions.yml"                           , emit: versions
 
     when:

tests/modules/gappa/examineassign/nextflow.config

@@ -2,8 +2,9 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    ext.args   = "--per-query-results"
 
     ext.when   = { taxonomy }
 
+    ext.args   = "--per-query-results --krona --sativa"
+    
 }

tests/modules/gappa/examineassign/test.yml

@@ -10,6 +10,9 @@
       md5sum: 16e1fbcc5f79588a0ed21e495cdd91ee
     - path: output/gappa/test.profile.tsv
       md5sum: ce604fa03604462358b69cfbff7c1593
+    - path: output/gappa/test.krona.profile
+      md5sum: 19110ac998eaa7532f2a92772cd35aa6
+    - path: output/gappa/test.sativa.tsv
+      md5sum: 28020fc2f8440fabb5ae83b0c7114cdb
     - path: output/gappa/versions.yml
-      contains:
-        - "0.8.0"
+      md5sum: a6a80882e5a6b76a412ba2378bb40b51