From e97d4cd32baf206903b8e15e0ff9b893ae8439d5 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Fri, 9 Sep 2022 09:54:03 +0200
Subject: [PATCH] epang: Output gzipped jplace (#2037)

* Output gzipped jplace
---
 modules/epang/main.nf        | 7 +++++--
 modules/epang/meta.yml       | 4 ++--
 tests/modules/epang/test.yml | 2 +-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/modules/epang/main.nf b/modules/epang/main.nf
index 8eaaa226..11d8dbea 100644
--- a/modules/epang/main.nf
+++ b/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}":
diff --git a/modules/epang/meta.yml b/modules/epang/meta.yml
index 18357b9e..c1418693 100644
--- a/modules/epang/meta.yml
+++ b/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
diff --git a/tests/modules/epang/test.yml b/tests/modules/epang/test.yml
index 84630b1f..b4b861c1 100644
--- a/tests/modules/epang/test.yml
+++ b/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 "}'