epang: Output gzipped jplace (#2037)

* Output gzipped jplace

modules/epang/main.nf

@@ -45,8 +45,11 @@ process EPANG {
         $splitarg \\
         $binaryarg
 
-    [ -e epa_result.jplace ] && mv epa_result.jplace ${prefix}.epa_result.jplace
-    [ -e epa_info.log ]      && mv epa_info.log      ${prefix}.epa_info.log
+    if [ -e epa_result.jplace ]; then
+        gzip epa_result.jplace
+        cp epa_result.jplace.gz ${prefix}.epa_result.jplace.gz
+    fi
+    [ -e epa_info.log ]      && cp epa_info.log ${prefix}.epa_info.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/epang/meta.yml

@@ -55,8 +55,8 @@ output:
       description: directory in which EPA-NG was run
   - jplace:
       type: file
-      description: file with placement information
-      pattern: "*.jplace"
+      description: gzipped file with placement information
+      pattern: "*.jplace.gz"
   - log:
       type: file
       description: log file from placement

tests/modules/epang/test.yml

@@ -6,7 +6,7 @@
     - path: output/epang/test.epa_info.log
       contains:
         - "INFO 3 Sequences done"
-    - path: output/epang/test.epa_result.jplace
+    - path: output/epang/test.epa_result.jplace.gz
       contains:
         - '"placements":'
         - '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}'