From 3531824af826c16cd252bc5aa82ae169b244ebaa Mon Sep 17 00:00:00 2001
From: Mahwash Jamy <40695699+mjamy@users.noreply.github.com>
Date: Thu, 14 Jul 2022 16:18:28 +0200
Subject: [PATCH] Update DIAMOND module to output log file (#1879)

* Update DIAMOND module to output log file

* Updating DIAMOND module to output log file - with jfy133 suggestions

Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/diamond/blastx/main.nf        |  6 +++++-
 modules/diamond/blastx/meta.yml       |  5 +++++
 tests/modules/diamond/blastx/test.yml | 13 ++++++++-----
 3 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index d3272279..1f4ff257 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -21,6 +21,7 @@ process DIAMOND_BLASTX {
     tuple val(meta), path('*.sam')  , optional: true, emit: sam
     tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
     tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    tuple val(meta), path("*.log")                  , emit: log
     path "versions.yml"                               , emit: versions
 
     when:
@@ -54,7 +55,10 @@ process DIAMOND_BLASTX {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${out_ext}
+        --out ${prefix}.${out_ext} \\
+        --log
+
+    mv diamond.log ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 2dcd7bc6..327b8937 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -70,7 +70,12 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - log:
+      type: file
+      description: Log file containing stdout information
+      pattern: "*.{log}"
 
 authors:
   - "@spficklin"
   - "@jfy133"
+  - "@mjamy"
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index b2b6149f..9f62d2ef 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -1,18 +1,21 @@
 - name: diamond blastx test_diamond_blastx
-  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
+    - path: output/diamond/proteome.fasta.dmnd
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]
     - path: output/diamond/test.diamond_blastx.txt
-    - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa
-  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c ./tests/config/nextflow.config  -c ./tests/modules/diamond/blastx/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
+    - path: output/diamond/proteome.fasta.dmnd
     - path: output/diamond/test.diamond_blastx.daa
-      md5sum: 0df4a833408416f32981415873facc11
-    - path: output/diamond/versions.yml
+    - path: output/diamond/test.diamond_blastx.log
+      contains: ["queries aligned"]