From 72b96f4e504eef673f2b5c13560a9d90b669129b Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 3 Mar 2022 17:58:04 +0100
Subject: [PATCH] Add missing $prefix definition for MALT_RUN (#1373)

* fix: remove left-over unnecessary code

* Add forgotten prefix for the log

* Update meta.yml

* Update tests

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
---
 modules/malt/run/main.nf        | 3 ++-
 modules/malt/run/meta.yml       | 2 +-
 tests/modules/malt/run/test.yml | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf
index 61c02ec1..4e2e50c9 100644
--- a/modules/malt/run/main.nf
+++ b/modules/malt/run/main.nf
@@ -23,6 +23,7 @@ process MALT_RUN {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def avail_mem = 6
     if (!task.memory) {
         log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@@ -39,7 +40,7 @@ process MALT_RUN {
         $args \\
         --inFile ${fastqs.join(' ')} \\
         -m $mode \\
-        --index $index/ |&tee malt-run.log
+        --index $index/ |&tee ${prefix}-malt-run.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/malt/run/meta.yml b/modules/malt/run/meta.yml
index ae4277a8..66f2d7a9 100644
--- a/modules/malt/run/meta.yml
+++ b/modules/malt/run/meta.yml
@@ -52,7 +52,7 @@ output:
   - log:
       type: file
       description: Log of verbose MALT stdout
-      pattern: "malt-run.log"
+      pattern: "*-malt-run.log"
 
 authors:
   - "@jfy133"
diff --git a/tests/modules/malt/run/test.yml b/tests/modules/malt/run/test.yml
index 335bc977..8ad44094 100644
--- a/tests/modules/malt/run/test.yml
+++ b/tests/modules/malt/run/test.yml
@@ -5,4 +5,4 @@
     - malt/run
   files:
     - path: output/malt/test_1.rma6
-    - path: output/malt/malt-run.log
+    - path: output/malt/test-malt-run.log